chr11-124748043-A-C

Variant names:

• chr11-124748043-A-C
• rs2075713
• NM_014312.5:c.851+347T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 13 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014312.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG2	NM_014312.5	MANE Select	c.851+347T>G		intron	N/A	NP_055127.2
	VSIG2	NM_001329920.2		c.*343T>G		downstream_gene	N/A	NP_001316849.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG2	ENST00000326621.10	TSL:1 MANE Select	c.851+347T>G		intron	N/A	ENSP00000318684.5
	VSIG2	ENST00000896674.1		c.852-334T>G		intron	N/A	ENSP00000566733.1
	VSIG2	ENST00000896673.1		c.782+347T>G		intron	N/A	ENSP00000566732.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31040 AN: 151890 Hom.: 3545 Cov.: 32

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

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

GnomAD4 genome AF: 0.204 AC: 31046 AN: 152008 Hom.: 3546 Cov.: 32 AF XY: 0.200 AC XY: 14854 AN XY: 74302

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: 54 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11511 AN: 67962

Other (OTH) AF: 0.177 AC: 374 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2075713; hg19: chr11-124617939;