12-118068522-TTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCC

Variant names:

• chr12-118068522-T-TTCCTCC
• rs67582641
• NM_019086.6:c.1416_1421dupGGAGGA

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_019086.6(VSIG10):​c.1416_1421dupGGAGGA​(p.Glu473_Glu474dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000363 in 1,602,506 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0017 (0 hom., cov: 19)
  • Exomes 𝑓: 0.00022 (0 hom.)
• Consequence: VSIG10 NM_019086.6 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• 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: Likely_benign. The variant received -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_019086.6

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10	NM_019086.6	MANE Select	c.1416_1421dupGGAGGA	p.Glu473_Glu474dup	disruptive_inframe_insertion	Exon 8 of 9	NP_061959.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10	ENST00000359236.10	TSL:1 MANE Select	c.1416_1421dupGGAGGA	p.Glu473_Glu474dup	disruptive_inframe_insertion	Exon 8 of 9	ENSP00000352172.5	Q8N0Z9-1
	VSIG10	ENST00000965107.1		c.1413_1418dupGGAGGA	p.Glu472_Glu473dup	disruptive_inframe_insertion	Exon 8 of 9	ENSP00000635166.1
	VSIG10	ENST00000965105.1		c.1155_1160dupGGAGGA	p.Glu386_Glu387dup	disruptive_inframe_insertion	Exon 7 of 8	ENSP00000635164.1

Frequencies

GnomAD3 genomes AF: 0.00173 AC: 260 AN: 150680 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00574

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00126

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000962

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000443

Gnomad OTH AF: 0.000969

GnomAD2 exomes AF: 0.000438 AC: 95 AN: 216714 AF XY: 0.000315

Gnomad AFR exome AF: 0.00554

Gnomad AMR exome AF: 0.000412

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000511

Gnomad OTH exome AF: 0.000566

GnomAD4 exome AF: 0.000222 AC: 322 AN: 1451714 Hom.: 0 Cov.: 29 AF XY: 0.000197 AC XY: 142 AN XY: 721578

African (AFR) AF: 0.00663 AC: 220 AN: 33176

American (AMR) AF: 0.000419 AC: 18 AN: 42976

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25942

East Asian (EAS) AF: 0.00 AC: 0 AN: 38980

South Asian (SAS) AF: 0.0000234 AC: 2 AN: 85300

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53060

Middle Eastern (MID) AF: 0.000695 AC: 4 AN: 5754

European-Non Finnish (NFE) AF: 0.0000361 AC: 40 AN: 1106506

Other (OTH) AF: 0.000633 AC: 38 AN: 60020

GnomAD4 genome AF: 0.00172 AC: 260 AN: 150792 Hom.: 0 Cov.: 19 AF XY: 0.00167 AC XY: 123 AN XY: 73574

African (AFR) AF: 0.00573 AC: 235 AN: 41030

American (AMR) AF: 0.00126 AC: 19 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5068

South Asian (SAS) AF: 0.00 AC: 0 AN: 4760

European-Finnish (FIN) AF: 0.0000962 AC: 1 AN: 10390

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000443 AC: 3 AN: 67696

Other (OTH) AF: 0.000959 AC: 2 AN: 2086

Alfa AF: 0.0000900 Hom.: 263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.36
Mutation Taster		=90/10	polymorphism

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;