chr11-124750251-G-T

Position:

• chr11-124750251-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014312.5(VSIG2):​c.428-385C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,106 control chromosomes in the GnomAD database, including 13,662 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 0.37 (13662 hom., cov: 32)
• Consequence: VSIG2 NM_014312.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSIG2	NM_014312.5	c.428-385C>A		intron_variant		ENST00000326621.10	NP_055127.2
VSIG2	NM_001329920.2	c.428-385C>A		intron_variant			NP_001316849.1
VSIG2	XM_047426684.1	c.428-385C>A		intron_variant			XP_047282640.1
VSIG2	XM_047426685.1	c.62-385C>A		intron_variant			XP_047282641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSIG2	ENST00000326621.10	c.428-385C>A		intron_variant		1	NM_014312.5	ENSP00000318684	P1
VSIG2	ENST00000403470.1	c.428-385C>A		intron_variant		2		ENSP00000385013

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56359 AN: 151988 Hom.: 13624 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.327

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.371 AC: 56440 AN: 152106 Hom.: 13662 Cov.: 32 AF XY: 0.363 AC XY: 27032 AN XY: 74366

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.323

Alfa AF: 0.267 Hom.: 10067

Bravo AF: 0.384

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.079
DANN	Benign	0.58

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: rs11219769; hg19: chr11-124620147;