Variant chr12-118068522-TTCCTCC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.61

Variant links:

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]

VSIG10 links:

LOC124903030 (HGNC:):

LOC124903030 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 linkuse as main transcript	c.1416_1421del	p.Glu473_Glu474del	inframe_deletion	8/9	ENST00000359236.10
LOC124903030	XR_007063479.1 linkuse as main transcript	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 linkuse as main transcript	c.1416_1421del	p.Glu473_Glu474del	inframe_deletion	8/9	1	NM_019086.6	P1	Q8N0Z9-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37042

AN:

150576

Hom.:

5071

Cov.:

show subpopulations

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

show subpopulations

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

show subpopulations

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.:

AF XY:

0.245

AC XY:

17979

AN XY:

73528

show subpopulations

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

LINK: link

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over