rs67582641
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019086.6(VSIG10):c.1410_1421del(p.Glu471_Glu474del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,602,398 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 0.0000066 ( 0 hom., cov: 19)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
VSIG10
NM_019086.6 inframe_deletion
NM_019086.6 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSIG10 | NM_019086.6 | c.1410_1421del | p.Glu471_Glu474del | inframe_deletion | 8/9 | ENST00000359236.10 | |
LOC124903030 | XR_007063479.1 | n.221+6857_221+6868del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSIG10 | ENST00000359236.10 | c.1410_1421del | p.Glu471_Glu474del | inframe_deletion | 8/9 | 1 | NM_019086.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000664 AC: 1AN: 150682Hom.: 0 Cov.: 19
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GnomAD3 exomes AF: 0.00000461 AC: 1AN: 216714Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 117466
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GnomAD4 exome AF: 0.0000110 AC: 16AN: 1451716Hom.: 0 AF XY: 0.0000111 AC XY: 8AN XY: 721578
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GnomAD4 genome ? AF: 0.00000664 AC: 1AN: 150682Hom.: 0 Cov.: 19 AF XY: 0.0000136 AC XY: 1AN XY: 73454
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at