1-145892806-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003637.5(ITGA10):c.3496G>A(p.Glu1166Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,612,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003637.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA10 | ENST00000369304.8 | c.3496G>A | p.Glu1166Lys | missense_variant | Exon 30 of 30 | 1 | NM_003637.5 | ENSP00000358310.3 | ||
ITGA10 | ENST00000539363.2 | c.3067G>A | p.Glu1023Lys | missense_variant | Exon 26 of 26 | 1 | ENSP00000439894.1 | |||
ENSG00000244619 | ENST00000415065.2 | n.-41C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251412Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135890
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1460436Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726666
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3496G>A (p.E1166K) alteration is located in exon 30 (coding exon 30) of the ITGA10 gene. This alteration results from a G to A substitution at nucleotide position 3496, causing the glutamic acid (E) at amino acid position 1166 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at