Variant rs72552763 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PM4_SupportingBA1

The ENST00000366963.9(SLC22A1):c.1260_1262del(p.Met420del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,526,850 control chromosomes in the GnomAD database, including 24,010 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1808 hom., cov: 28)

Exomes 𝑓: 0.17 ( 22202 hom. )

Consequence

SLC22A1
ENST00000366963.9 inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.20

Variant links:

Genes affected

SLC22A1 (HGNC:10963): (solute carrier family 22 member 1) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter. [provided by RefSeq, Jul 2008]

SLC22A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in ENST00000366963.9. Strenght limited to Supporting due to length of the change: 1aa.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC22A1	NM_003057.3 linkuse as main transcript	c.1260_1262del	p.Met420del	inframe_deletion	7/11	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2 linkuse as main transcript	c.1260_1262del	p.Met420del	inframe_deletion	7/10		NP_694857.1
SLC22A1	XM_005267103.3 linkuse as main transcript	c.1260_1262del	p.Met420del	inframe_deletion	7/12		XP_005267160.1
SLC22A1	XM_006715552.3 linkuse as main transcript	c.1260_1262del	p.Met420del	inframe_deletion	7/9		XP_006715615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9 linkuse as main transcript	c.1260_1262del	p.Met420del	inframe_deletion	7/11	1	NM_003057.3	ENSP00000355930	P1	O15245-1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

21145

AN:

139762

Hom.:

1799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0691

Gnomad AMI

AF:

0.0876

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.00274

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.163

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.162

GnomAD3 exomes

AF:

0.121

AC:

18010

AN:

148824

Hom.:

1455

AF XY:

0.122

AC XY:

9811

AN XY:

80508

show subpopulations

Gnomad AFR exome

AF:

0.0458

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.0883

Gnomad EAS exome

AF:

0.000695

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.172

AC:

239089

AN:

1386984

Hom.:

22202

AF XY:

0.172

AC XY:

117891

AN XY:

684456

show subpopulations

Gnomad4 AFR exome

AF:

0.0562

Gnomad4 AMR exome

AF:

0.262

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.000521

Gnomad4 SAS exome

AF:

0.171

Gnomad4 FIN exome

AF:

0.144

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.158

GnomAD4 genome

AF:

0.151

AC:

21167

AN:

139866

Hom.:

1808

Cov.:

AF XY:

0.153

AC XY:

10385

AN XY:

68086

show subpopulations

Gnomad4 AFR

AF:

0.0691

Gnomad4 AMR

AF:

0.244

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.00274

Gnomad4 SAS

AF:

0.178

Gnomad4 FIN

AF:

0.166

Gnomad4 NFE

AF:

0.183

Gnomad4 OTH

AF:

0.161

Alfa

AF:

0.134

Hom.:

320

Bravo

AF:

0.141

Asia WGS

AF:

0.0680

AC:

237

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over