NM_019086.6:c.1416_1421delGGAGGA

Variant names:

• chr12-118068522-TTCCTCC-T
• rs67582641
• NM_019086.6:c.1416_1421delGGAGGA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_019086.6(VSIG10):​c.1416_1421delGGAGGA​(p.Glu473_Glu474del) variant causes a disruptive 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 disruptive_inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.61
• Publications: 3 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]

LOC124903030 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 12-118068522-TTCCTCC-T is Benign according to our data. Variant chr12-118068522-TTCCTCC-T is described in CliVar as Benign. Clinvar id is 403604.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-118068522-TTCCTCC-T is described in CliVar as Benign. Clinvar id is 403604.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-118068522-TTCCTCC-T is described in CliVar as Benign. Clinvar id is 403604.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-118068522-TTCCTCC-T is described in CliVar as Benign. Clinvar id is 403604.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-118068522-TTCCTCC-T is described in CliVar 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 rank	MANE	Protein	UniProt
VSIG10	NM_019086.6	c.1416_1421delGGAGGA	p.Glu473_Glu474del	disruptive_inframe_deletion	Exon 8 of 9	ENST00000359236.10	NP_061959.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSIG10	ENST00000359236.10	c.1416_1421delGGAGGA	p.Glu473_Glu474del	disruptive_inframe_deletion	Exon 8 of 9	1	NM_019086.6	ENSP00000352172.5

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

GnomAD2 exomes AF: 0.229 AC: 49617 AN: 216714 AF XY: 0.225

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 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

African (AFR) AF: 0.330 AC: 10961 AN: 33176

American (AMR) AF: 0.201 AC: 8640 AN: 42964

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 4519 AN: 25942

East Asian (EAS) AF: 0.501 AC: 19512 AN: 38976

South Asian (SAS) AF: 0.206 AC: 17575 AN: 85286

European-Finnish (FIN) AF: 0.179 AC: 9478 AN: 53052

Middle Eastern (MID) AF: 0.200 AC: 1151 AN: 5750

European-Non Finnish (NFE) AF: 0.189 AC: 208577 AN: 1106258

Other (OTH) AF: 0.213 AC: 12779 AN: 60004

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

African (AFR) AF: 0.332 AC: 13592 AN: 40990

American (AMR) AF: 0.232 AC: 3497 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3462

East Asian (EAS) AF: 0.532 AC: 2695 AN: 5062

South Asian (SAS) AF: 0.216 AC: 1029 AN: 4758

European-Finnish (FIN) AF: 0.181 AC: 1877 AN: 10384

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12798 AN: 67666

Other (OTH) AF: 0.263 AC: 548 AN: 2086

Alfa AF: 0.130 Hom.: 263

Bravo AF: 0.260

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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
PhyloP100		1.6
Mutation Taster		=191/9	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs67582641; hg19: chr12-118506327; COSMIC: COSV63654088; COSMIC: COSV63654088;