Name: rs67666821
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs67666821

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:99758184-99758188 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delT / dupT
Variation Type: Indel Insertion and Deletion
Frequency: dupT=0.00006 (5/86014, ALFA)
dupT=0.00072 (9/12518, GO-ESP)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CYP3A4 : Frameshift Variant
Publications: 4 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	86014	TTTTT=0.99994	TTTT=0.00000, TTTTTT=0.00006
European	Sub	73142	TTTTT=0.99993	TTTT=0.00000, TTTTTT=0.00007
African	Sub	4200	TTTTT=1.0000	TTTT=0.0000, TTTTTT=0.0000
African Others	Sub	166	TTTTT=1.000	TTTT=0.000, TTTTTT=0.000
African American	Sub	4034	TTTTT=1.0000	TTTT=0.0000, TTTTTT=0.0000
Asian	Sub	3316	TTTTT=1.0000	TTTT=0.0000, TTTTTT=0.0000
East Asian	Sub	2662	TTTTT=1.0000	TTTT=0.0000, TTTTTT=0.0000
Other Asian	Sub	654	TTTTT=1.000	TTTT=0.000, TTTTTT=0.000
Latin American 1	Sub	434	TTTTT=1.000	TTTT=0.000, TTTTTT=0.000
Latin American 2	Sub	924	TTTTT=1.000	TTTT=0.000, TTTTTT=0.000
South Asian	Sub	270	TTTTT=1.000	TTTT=0.000, TTTTTT=0.000
Other	Sub	3728	TTTTT=1.0000	TTTT=0.0000, TTTTTT=0.0000

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	86014	(T)₅=0.99994	delT=0.00000, dupT=0.00006
Allele Frequency Aggregator	European	Sub	73142	(T)₅=0.99993	delT=0.00000, dupT=0.00007
Allele Frequency Aggregator	African	Sub	4200	(T)₅=1.0000	delT=0.0000, dupT=0.0000
Allele Frequency Aggregator	Other	Sub	3728	(T)₅=1.0000	delT=0.0000, dupT=0.0000
Allele Frequency Aggregator	Asian	Sub	3316	(T)₅=1.0000	delT=0.0000, dupT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	924	(T)₅=1.000	delT=0.000, dupT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	434	(T)₅=1.000	delT=0.000, dupT=0.000
Allele Frequency Aggregator	South Asian	Sub	270	(T)₅=1.000	delT=0.000, dupT=0.000
GO Exome Sequencing Project	Global	Study-wide	12518	- No frequency provided	dupT=0.00072
GO Exome Sequencing Project	European American	Sub	8254	- No frequency provided	dupT=0.0010
GO Exome Sequencing Project	African American	Sub	4264	- No frequency provided	dupT=0.0002

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 7	NC_000007.14:g.99758188del
GRCh38.p14 chr 7	NC_000007.14:g.99758188dup
GRCh37.p13 chr 7	NC_000007.13:g.99355811del
GRCh37.p13 chr 7	NC_000007.13:g.99355811dup
CYP3A4 RefSeqGene	NG_008421.1:g.31002del
CYP3A4 RefSeqGene	NG_008421.1:g.31002dup

Gene: CYP3A4, cytochrome P450 family 3 subfamily A member 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP3A4 transcript variant 1	NM_017460.6:c.1461del	K [AAA] > N [AA]	Coding Sequence Variant
cytochrome P450 3A4 isoform 1	NP_059488.2:p.Lys487fs	K (Lys) > N (Asn)	Frameshift Variant
CYP3A4 transcript variant 1	NM_017460.6:c.1461dup	P [CCC] > T [ACCC]	Coding Sequence Variant
cytochrome P450 3A4 isoform 1	NP_059488.2:p.Pro488fs	P (Pro) > T (Thr)	Frameshift Variant
CYP3A4 transcript variant 2	NM_001202855.3:c.1458del	K [AAA] > N [AA]	Coding Sequence Variant
cytochrome P450 3A4 isoform 2	NP_001189784.1:p.Lys486fs	K (Lys) > N (Asn)	Frameshift Variant
CYP3A4 transcript variant 2	NM_001202855.3:c.1458dup	P [CCC] > T [ACCC]	Coding Sequence Variant
cytochrome P450 3A4 isoform 2	NP_001189784.1:p.Pro487fs	P (Pro) > T (Thr)	Frameshift Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: dupT (allele ID: 1309206 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001752887.1	not provided	Likely-Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	(T)₅=	delT	dupT
GRCh38.p14 chr 7	NC_000007.14:g.99758184_99758188=	NC_000007.14:g.99758188del	NC_000007.14:g.99758188dup
GRCh37.p13 chr 7	NC_000007.13:g.99355807_99355811=	NC_000007.13:g.99355811del	NC_000007.13:g.99355811dup
CYP3A4 RefSeqGene	NG_008421.1:g.30998_31002=	NG_008421.1:g.31002del	NG_008421.1:g.31002dup
CYP3A4 transcript variant 1	NM_017460.6:c.1457_1461=	NM_017460.6:c.1461del	NM_017460.6:c.1461dup
CYP3A4 transcript variant 1	NM_017460.5:c.1457_1461=	NM_017460.5:c.1461del	NM_017460.5:c.1461dup
CYP3A4 transcript variant 2	NM_001202855.3:c.1454_1458=	NM_001202855.3:c.1458del	NM_001202855.3:c.1458dup
CYP3A4 transcript variant 2	NM_001202855.2:c.1454_1458=	NM_001202855.2:c.1458del	NM_001202855.2:c.1458dup
CYP3A4 transcript variant 3	NM_001202856.1:c.1310_1314=	NM_001202856.1:c.1314del	NM_001202856.1:c.1314dup
CYP3A4 transcript variant 4	NM_001202857.1:c.1007_1011=	NM_001202857.1:c.1011del	NM_001202857.1:c.1011dup
CYP3A3 transcript	NM_000776.1:c.1460_1464=	NM_000776.1:c.1464del	NM_000776.1:c.1464dup
cytochrome P450 3A4 isoform 1	NP_059488.2:p.Glu486_Lys487=	NP_059488.2:p.Lys487fs	NP_059488.2:p.Pro488fs
cytochrome P450 3A4 isoform 2	NP_001189784.1:p.Glu485_Lys486=	NP_001189784.1:p.Lys486fs	NP_001189784.1:p.Pro487fs

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

18 SubSNP, 14 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	CNG	ss98335841	Feb 06, 2009 (130)
2	AFFY_DM3_1	ss105434727	Feb 06, 2009 (130)
3	EVA_DECODE	ss1594169755	Apr 01, 2015 (144)
4	EVA_UK10K_ALSPAC	ss1705749512	Apr 01, 2015 (144)
5	EVA_UK10K_TWINSUK	ss1705749737	Apr 01, 2015 (144)
6	EVA_UK10K_ALSPAC	ss1710339745	Apr 01, 2015 (144)
7	EVA_UK10K_TWINSUK	ss1710343555	Apr 01, 2015 (144)
8	EVA_EXAC	ss1711863003	Apr 01, 2015 (144)
9	EVA_EXAC	ss1711863004	Apr 01, 2015 (144)
10	ILLUMINA	ss2711117378	Nov 08, 2017 (151)
11	GNOMAD	ss2747872084	Nov 08, 2017 (151)
12	GNOMAD	ss2856772096	Nov 08, 2017 (151)
13	EVA_DECODE	ss3720301913	Jul 13, 2019 (153)
14	EVA	ss3824296541	Apr 26, 2020 (154)
15	GNOMAD	ss4169406615	Apr 26, 2021 (155)
16	TOPMED	ss4756585696	Apr 26, 2021 (155)
17	TOPMED	ss4756585697	Apr 26, 2021 (155)
18	HUGCELL_USP	ss5471004559	Oct 17, 2022 (156)
19	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 21342139 (NC_000007.13:99355806:T: 1/3854) Row 21342140 (NC_000007.13:99355806::T 2/3854)	-	Oct 12, 2018 (152)
20	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 21342139 (NC_000007.13:99355806:T: 1/3854) Row 21342140 (NC_000007.13:99355806::T 2/3854)	-	Oct 12, 2018 (152)
21	ExAC Submission ignored due to conflicting rows: Row 8915641 (NC_000007.13:99355806:T: 1/121250) Row 8915642 (NC_000007.13:99355806::T 34/121250)	-	Oct 12, 2018 (152)
22	ExAC Submission ignored due to conflicting rows: Row 8915641 (NC_000007.13:99355806:T: 1/121250) Row 8915642 (NC_000007.13:99355806::T 34/121250)	-	Oct 12, 2018 (152)
23	gnomAD - Genomes Submission ignored due to conflicting rows: Row 270655568 (NC_000007.14:99758183::T 52/140196) Row 270655569 (NC_000007.14:99758183:T: 4/140196)	-	Apr 26, 2021 (155)
24	gnomAD - Genomes Submission ignored due to conflicting rows: Row 270655568 (NC_000007.14:99758183::T 52/140196) Row 270655569 (NC_000007.14:99758183:T: 4/140196)	-	Apr 26, 2021 (155)
25	gnomAD - Exomes Submission ignored due to conflicting rows: Row 5764157 (NC_000007.13:99355806::T 86/251248) Row 5764158 (NC_000007.13:99355806:T: 1/251248)	-	Jul 13, 2019 (153)
26	gnomAD - Exomes Submission ignored due to conflicting rows: Row 5764157 (NC_000007.13:99355806::T 86/251248) Row 5764158 (NC_000007.13:99355806:T: 1/251248)	-	Jul 13, 2019 (153)
27	GO Exome Sequencing Project	NC_000007.13 - 99355807	Oct 12, 2018 (152)
28	TopMed Submission ignored due to conflicting rows: Row 593963255 (NC_000007.14:99758183::T 140/264690) Row 593963256 (NC_000007.14:99758183:T: 4/264690)	-	Apr 26, 2021 (155)
29	TopMed Submission ignored due to conflicting rows: Row 593963255 (NC_000007.14:99758183::T 140/264690) Row 593963256 (NC_000007.14:99758183:T: 4/264690)	-	Apr 26, 2021 (155)
30	UK 10K study - Twins Submission ignored due to conflicting rows: Row 21342139 (NC_000007.13:99355806:T: 0/3708) Row 21342140 (NC_000007.13:99355806::T 1/3708)	-	Oct 12, 2018 (152)
31	UK 10K study - Twins Submission ignored due to conflicting rows: Row 21342139 (NC_000007.13:99355806:T: 0/3708) Row 21342140 (NC_000007.13:99355806::T 1/3708)	-	Oct 12, 2018 (152)
32	ALFA	NC_000007.14 - 99758184	Apr 26, 2021 (155)
33	ClinVar	RCV001752887.1	Oct 17, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs67666822	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1705749512, ss1705749737, ss1711863004	NC_000007.13:99355806:T:	NC_000007.14:99758183:TTTTT:TTTT	(self)
ss4169406615, ss4756585697	NC_000007.14:99758183:T:	NC_000007.14:99758183:TTTTT:TTTT	(self)
5621988850	NC_000007.14:99758183:TTTTT:TTTT	NC_000007.14:99758183:TTTTT:TTTT	(self)
ss1594169755	NC_000007.12:99193742::T	NC_000007.14:99758183:TTTTT:TTTTTT	(self)
754485, ss1711863003, ss2711117378, ss2747872084, ss2856772096, ss3824296541	NC_000007.13:99355806::T	NC_000007.14:99758183:TTTTT:TTTTTT	(self)
ss1710339745, ss1710343555	NC_000007.13:99355807::T	NC_000007.14:99758183:TTTTT:TTTTTT	(self)
ss3720301913, ss4756585696, ss5471004559	NC_000007.14:99758183::T	NC_000007.14:99758183:TTTTT:TTTTTT	(self)
RCV001752887.1, 5621988850	NC_000007.14:99758183:TTTTT:TTTTTT	NC_000007.14:99758183:TTTTT:TTTTTT	(self)
ss98335841, ss105434727	NT_007933.15:37388649::T	NC_000007.14:99758183:TTTTT:TTTTTT	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs67666821

PMID	Title	Author	Year	Journal
21790905	CYP2B6 SNPs are associated with methadone dose required for effective treatment of opioid addiction.	Levran O et al.	2013	Addiction biology
29256966	Influence of donor liver CYP3A4*20 loss-of-function genotype on tacrolimus pharmacokinetics in transplanted patients.	Gómez-Bravo MA et al.	2018	Pharmacogenetics and genomics
29469606	Detection of a rare CYP3A4 variant in a transplant patient characterized by a tacrolimus poor metabolizer phenotype.	Lloberas N et al.	2018	Pharmacogenomics
35335935	Role of Pharmacogenetics in the Treatment of Acute Myeloid Leukemia: Systematic Review and Future Perspectives.	Pinto-Merino Á et al.	2022	Pharmaceutics

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs67666821