rs2075713

chr11-124748043-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

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	UniProt
VSIG2	NM_014312.5	c.851+347T>G		intron_variant		ENST00000326621.10
VSIG2	XM_047426685.1	c.485+347T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSIG2	ENST00000326621.10	c.851+347T>G		intron_variant		1	NM_014312.5	P1

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

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.: 32 AF XY: 0.200 AC XY: 14854 AN XY: 74302

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	13
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

Other links and lift over

dbSNP: rs2075713; hg19: chr11-124617939;