Variant 6-160122091-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003057.3(SLC22A1):c.156T>C(p.Ser52Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,613,736 control chromosomes in the GnomAD database, including 40,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4864 hom., cov: 33)

Exomes 𝑓: 0.22 ( 35698 hom. )

Consequence

SLC22A1
NM_003057.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.150

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP7

Synonymous conserved (PhyloP=0.15 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A1	NM_003057.3 linkuse as main transcript	c.156T>C	p.Ser52Ser	synonymous_variant	1/11	ENST00000366963.9	NP_003048.1	O15245-1
SLC22A1	NM_153187.2 linkuse as main transcript	c.156T>C	p.Ser52Ser	synonymous_variant	1/10		NP_694857.1	O15245-2
SLC22A1	XM_005267103.3 linkuse as main transcript	c.156T>C	p.Ser52Ser	synonymous_variant	1/12		XP_005267160.1
SLC22A1	XM_006715552.3 linkuse as main transcript	c.156T>C	p.Ser52Ser	synonymous_variant	1/9		XP_006715615.1	O15245-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9 linkuse as main transcript	c.156T>C	p.Ser52Ser	synonymous_variant	1/11	1	NM_003057.3	ENSP00000355930.4		O15245-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37351

AN:

152040

Hom.:

4852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.240

GnomAD3 exomes

AF:

0.249

AC:

62439

AN:

251230

Hom.:

8350

AF XY:

0.239

AC XY:

32529

AN XY:

135822

show subpopulations

Gnomad AFR exome

AF:

0.308

Gnomad AMR exome

AF:

0.354

Gnomad ASJ exome

AF:

0.135

Gnomad EAS exome

AF:

0.398

Gnomad SAS exome

AF:

0.202

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.212

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.216

AC:

316151

AN:

1461578

Hom.:

35698

Cov.:

AF XY:

0.215

AC XY:

156349

AN XY:

727098

show subpopulations

Gnomad4 AFR exome

AF:

0.308

Gnomad4 AMR exome

AF:

0.344

Gnomad4 ASJ exome

AF:

0.135

Gnomad4 EAS exome

AF:

0.395

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.218

Gnomad4 NFE exome

AF:

0.205

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.246

AC:

37410

AN:

152158

Hom.:

4864

Cov.:

AF XY:

0.245

AC XY:

18242

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.274

Gnomad4 ASJ

AF:

0.137

Gnomad4 EAS

AF:

0.391

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.214

Hom.:

3701

Bravo

AF:

0.258

Asia WGS

AF:

0.311

AC:

1085

AN:

3478

EpiCase

AF:

0.213

EpiControl

AF:

0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

2.4

DANN

Benign

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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