Variant rs2075713 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014312.5(VSIG2):c.851+347T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 351,928 control chromosomes in the GnomAD database, including 6,800 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 0.20 ( 3546 hom., cov: 32)

Exomes 𝑓: 0.17 ( 3254 hom. )

Consequence

VSIG2
NM_014312.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Variant links:

Genes affected

VSIG2 (HGNC:17149): (V-set and immunoglobulin domain containing 2) Predicted to be located in membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

VSIG2 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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSIG2	NM_014312.5 linkuse as main transcript	c.851+347T>G		intron_variant		ENST00000326621.10	NP_055127.2
VSIG2	XM_047426685.1 linkuse as main transcript	c.485+347T>G		intron_variant			XP_047282641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSIG2	ENST00000326621.10 linkuse as main transcript	c.851+347T>G		intron_variant		1	NM_014312.5	ENSP00000318684	P1	Q96IQ7-1

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

31040

AN:

151890

Hom.:

3545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.180

GnomAD4 exome

AF:

0.170

AC:

34058

AN:

199920

Hom.:

3254

AF XY:

0.170

AC XY:

17431

AN XY:

102578

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.110

Gnomad4 ASJ exome

AF:

0.248

Gnomad4 EAS exome

AF:

0.187

Gnomad4 SAS exome

AF:

0.161

Gnomad4 FIN exome

AF:

0.177

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.204

AC:

31046

AN:

152008

Hom.:

3546

Cov.:

AF XY:

0.200

AC XY:

14854

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.310

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.173

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.169

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.174

Hom.:

4992

Bravo

AF:

0.206

Asia WGS

AF:

0.137

AC:

475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.87

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