12-118086621-A-G

Variant names:

• chr12-118086621-A-G
• rs7957470
• NM_019086.6:c.362-4192T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019086.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10	NM_019086.6	MANE Select	c.362-4192T>C		intron	N/A	NP_061959.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10	ENST00000359236.10	TSL:1 MANE Select	c.362-4192T>C		intron	N/A	ENSP00000352172.5
	VSIG10	ENST00000538357.1	TSL:2	c.362-7015T>C		intron	N/A	ENSP00000442861.1
	VSIG10	ENST00000536905.5	TSL:5	n.873-4192T>C		intron	N/A

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

African (AFR) AF: 0.376 AC: 15569 AN: 41412

American (AMR) AF: 0.322 AC: 4903 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1727 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1105 AN: 5182

South Asian (SAS) AF: 0.435 AC: 2092 AN: 4812

European-Finnish (FIN) AF: 0.461 AC: 4863 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29564 AN: 67936

Other (OTH) AF: 0.365 AC: 767 AN: 2104

Alfa AF: 0.416 Hom.: 34413

Bravo AF: 0.386

Asia WGS AF: 0.363 AC: 1260 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.30
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: rs7957470; hg19: chr12-118524426;