Variant 6-160224800-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003058.4(SLC22A2):c.1506G>A(p.Val502Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 1,572,278 control chromosomes in the GnomAD database, including 459,886 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 0.70 ( 39330 hom., cov: 32)

Exomes 𝑓: 0.77 ( 420556 hom. )

Consequence

SLC22A2
NM_003058.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Variant links:

Genes affected

SLC22A2 (HGNC:10966): (solute carrier family 22 member 2) 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. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

SLC22A2 links:

SLC22A2 (HGNC:):

SLC22A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A2	NM_003058.4 linkuse as main transcript	c.1506G>A	p.Val502Val	synonymous_variant	10/11	ENST00000366953.8	NP_003049.2	O15244-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC22A2	ENST00000366953.8 linkuse as main transcript	c.1506G>A	p.Val502Val	synonymous_variant	10/11	1	NM_003058.4	ENSP00000355920.3	O15244-1
SLC22A2	ENST00000486916.5 linkuse as main transcript	n.545G>A		non_coding_transcript_exon_variant	5/6	3
SLC22A2	ENST00000491092.1 linkuse as main transcript	n.1403G>A		non_coding_transcript_exon_variant	9/10	5

Frequencies

GnomAD3 genomes

AF:

0.704

AC:

106920

AN:

151968

Hom.:

39308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.839

Gnomad AMR

AF:

0.816

Gnomad ASJ

AF:

0.793

Gnomad EAS

AF:

0.799

Gnomad SAS

AF:

0.790

Gnomad FIN

AF:

0.847

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.776

Gnomad OTH

AF:

0.728

GnomAD3 exomes

AF:

0.776

AC:

185325

AN:

238764

Hom.:

73047

AF XY:

0.780

AC XY:

100871

AN XY:

129302

show subpopulations

Gnomad AFR exome

AF:

0.462

Gnomad AMR exome

AF:

0.886

Gnomad ASJ exome

AF:

0.792

Gnomad EAS exome

AF:

0.799

Gnomad SAS exome

AF:

0.782

Gnomad FIN exome

AF:

0.838

Gnomad NFE exome

AF:

0.770

Gnomad OTH exome

AF:

0.782

GnomAD4 exome

AF:

0.767

AC:

1088868

AN:

1420192

Hom.:

420556

Cov.:

AF XY:

0.769

AC XY:

543246

AN XY:

706662

show subpopulations

Gnomad4 AFR exome

AF:

0.454

Gnomad4 AMR exome

AF:

0.875

Gnomad4 ASJ exome

AF:

0.792

Gnomad4 EAS exome

AF:

0.821

Gnomad4 SAS exome

AF:

0.781

Gnomad4 FIN exome

AF:

0.836

Gnomad4 NFE exome

AF:

0.766

Gnomad4 OTH exome

AF:

0.754

GnomAD4 genome

AF:

0.703

AC:

106983

AN:

152086

Hom.:

39330

Cov.:

AF XY:

0.711

AC XY:

52859

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.473

Gnomad4 AMR

AF:

0.817

Gnomad4 ASJ

AF:

0.793

Gnomad4 EAS

AF:

0.800

Gnomad4 SAS

AF:

0.791

Gnomad4 FIN

AF:

0.847

Gnomad4 NFE

AF:

0.776

Gnomad4 OTH

AF:

0.731

Alfa

AF:

0.769

Hom.:

101815

Bravo

AF:

0.692

Asia WGS

AF:

0.796

AC:

2769

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.51

DANN

Benign

0.55

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