Genetic Variant NM_014312.5:c.851+347T>G (chr11-124748043-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

13 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
VSIG2	NM_014312.5 link	c.851+347T>G	intron_variant	Intron 6 of 6	ENST00000326621.10	NP_055127.2	Q96IQ7-1
VSIG2	XM_047426685.1 link	c.485+347T>G	intron_variant	Intron 4 of 4		XP_047282641.1
VSIG2	NM_001329920.2 link	c.*343T>G	downstream_gene_variant			NP_001316849.1	Q96IQ7-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSIG2	ENST00000326621.10 link	c.851+347T>G		intron_variant	Intron 6 of 6	1	NM_014312.5	ENSP00000318684.5		Q96IQ7-1
VSIG2	ENST00000403470.1 link	c.*343T>G		downstream_gene_variant		2		ENSP00000385013.1		Q96IQ7-2

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

African (AFR)

AF:

0.294

AC:

1669

AN:

5684

American (AMR)

AF:

0.110

AC:

764

AN:

6918

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

1691

AN:

6816

East Asian (EAS)

AF:

0.187

AC:

2255

AN:

12078

South Asian (SAS)

AF:

0.161

AC:

2428

AN:

15078

European-Finnish (FIN)

AF:

0.177

AC:

2130

AN:

12018

Middle Eastern (MID)

AF:

0.183

AC:

175

AN:

958

European-Non Finnish (NFE)

AF:

0.162

AC:

20698

AN:

127538

Other (OTH)

AF:

0.175

AC:

2248

AN:

12832

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1347

2694

4041

5388

6735

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

264

396

528

660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.204

AC:

31046

AN:

152008

Hom.:

3546

Cov.:

AF XY:

0.200

AC XY:

14854

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.310

AC:

12845

AN:

41414

American (AMR)

AF:

0.125

AC:

1910

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

870

AN:

3458

East Asian (EAS)

AF:

0.138

AC:

713

AN:

5178

South Asian (SAS)

AF:

0.173

AC:

834

AN:

4816

European-Finnish (FIN)

AF:

0.179

AC:

1896

AN:

10582

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11511

AN:

67962

Other (OTH)

AF:

0.177

AC:

374

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1252

2505

3757

5010

6262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

328

656

984

1312

1640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.182

Hom.:

8970

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

(source)

DANN

Benign

0.87

PhyloP100

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over