12-118086621-A-G

Variant summary

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

The NM_019086.6(VSIG10):c.362-4192T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,892 control chromosomes in the GnomAD database, including 12,472 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 0.40 (12472 hom., cov: 31)
• Consequence: VSIG10 NM_019086.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

VSIG10 (HGNC:26078): (V-set and immunoglobulin domain containing 10) Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be active in cell-cell junction. 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VSIG10	NM_019086.6	c.362-4192T>C		intron_variant		ENST00000359236.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSIG10	ENST00000359236.10	c.362-4192T>C		intron_variant		1	NM_019086.6	P1
VSIG10	ENST00000538357.1	c.362-7015T>C		intron_variant		2
VSIG10	ENST00000536905.5	n.873-4192T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60970 AN: 151774 Hom.: 12469 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.402 AC: 61004 AN: 151892 Hom.: 12472 Cov.: 31 AF XY: 0.399 AC XY: 29596 AN XY: 74242

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.365

Alfa AF: 0.421 Hom.: 13168

Bravo AF: 0.386

Asia WGS AF: 0.363 AC: 1260 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.33

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: rs7957470; hg19: chr12-118524426;