Variant 6-160275887-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000419196.1(ENSG00000230234):n.224C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,302 control chromosomes in the GnomAD database, including 270 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 0.050 ( 270 hom., cov: 32)

Exomes 𝑓: 0.15 ( 0 hom. )

Consequence

ENST00000419196.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.41

Variant links:

Genes affected

(HGNC:):

links:

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.23).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378088	XR_001744437.2 linkuse as main transcript	n.262C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000419196.1 linkuse as main transcript	n.224C>T		non_coding_transcript_exon_variant	2/2	3
SLC22A2	ENST00000366952.1 linkuse as main transcript	c.-1297+1566G>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0497

AC:

7566

AN:

152138

Hom.:

270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0125

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0116

Gnomad FIN

AF:

0.0578

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0765

Gnomad OTH

AF:

0.0482

GnomAD4 exome

AF:

0.152

AC:

AN:

Hom.:

Cov.:

AF XY:

0.192

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.158

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0497

AC:

7567

AN:

152256

Hom.:

270

Cov.:

AF XY:

0.0466

AC XY:

3469

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0124

Gnomad4 AMR

AF:

0.0368

Gnomad4 ASJ

AF:

0.131

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0120

Gnomad4 FIN

AF:

0.0578

Gnomad4 NFE

AF:

0.0765

Gnomad4 OTH

AF:

0.0477

Alfa

AF:

0.0686

Hom.:

242

Bravo

AF:

0.0485

Asia WGS

AF:

0.0100

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.91

Splicing

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