12-118081636-T-C

Variant names:

• chr12-118081636-T-C
• rs4767658
• NM_019086.6:c.664+491A>G

Variant summary

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

The NM_019086.6(VSIG10):​c.664+491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,100 control chromosomes in the GnomAD database, including 14,886 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 0.44 (14886 hom., cov: 32)
• Consequence: VSIG10 NM_019086.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSIG10	NM_019086.6	c.664+491A>G		intron_variant	Intron 3 of 8	ENST00000359236.10	NP_061959.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSIG10	ENST00000359236.10	c.664+491A>G		intron_variant	Intron 3 of 8	1	NM_019086.6	ENSP00000352172.5
VSIG10	ENST00000538357.1	c.362-2030A>G		intron_variant	Intron 2 of 2	2		ENSP00000442861.1
VSIG10	ENST00000545722.1	n.127+516A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66466 AN: 151982 Hom.: 14874 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.437 AC: 66517 AN: 152100 Hom.: 14886 Cov.: 32 AF XY: 0.440 AC XY: 32677 AN XY: 74336

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.470

Alfa AF: 0.412 Hom.: 17456

Bravo AF: 0.457

Asia WGS AF: 0.416 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.81

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: rs4767658; hg19: chr12-118519441;