12-118068522-TTCCTCC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_019086.6(VSIG10):c.1416_1421del(p.Glu473_Glu474del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,602,096 control chromosomes in the GnomAD database, including 35,263 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.25 (5081 hom., cov: 19)
  • Exomes 𝑓: 0.20 (30182 hom.)
• Consequence: VSIG10 NM_019086.6 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.61

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]

LOC124903030 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-118068522-TTCCTCC-T is Benign according to our data. Variant chr12-118068522-TTCCTCC-T is described in ClinVar as [Benign]. Clinvar id is 403604.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VSIG10	NM_019086.6	c.1416_1421del	p.Glu473_Glu474del	inframe_deletion	8/9	ENST00000359236.10
LOC124903030	XR_007063479.1	n.221+6863_221+6868del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSIG10	ENST00000359236.10	c.1416_1421del	p.Glu473_Glu474del	inframe_deletion	8/9	1	NM_019086.6	P1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37042 AN: 150576 Hom.: 5071 Cov.: 19

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.266

GnomAD3 exomes AF: 0.229 AC: 49617 AN: 216714 Hom.: 5967 AF XY: 0.225 AC XY: 26390 AN XY: 117466

Gnomad AFR exome AF: 0.338

Gnomad AMR exome AF: 0.213

Gnomad ASJ exome AF: 0.179

Gnomad EAS exome AF: 0.518

Gnomad SAS exome AF: 0.217

Gnomad FIN exome AF: 0.184

Gnomad NFE exome AF: 0.190

Gnomad OTH exome AF: 0.231

GnomAD4 exome AF: 0.202 AC: 293192 AN: 1451408 Hom.: 30182 AF XY: 0.202 AC XY: 145441 AN XY: 721440

Gnomad4 AFR exome AF: 0.330

Gnomad4 AMR exome AF: 0.201

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.501

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.179

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.246 AC: 37077 AN: 150688 Hom.: 5081 Cov.: 19 AF XY: 0.245 AC XY: 17979 AN XY: 73528

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.263

Bravo AF: 0.260

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs67582641; hg19: chr12-118506327;