1-145896844-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003637.5(ITGA10):c.2759G>A(p.Arg920Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R920I) has been classified as Uncertain significance.
Frequency
Consequence
NM_003637.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA10 | ENST00000369304.8 | c.2759G>A | p.Arg920Lys | missense_variant | Exon 23 of 30 | 1 | NM_003637.5 | ENSP00000358310.3 | ||
ITGA10 | ENST00000539363.2 | c.2330G>A | p.Arg777Lys | missense_variant | Exon 19 of 26 | 1 | ENSP00000439894.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251378Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135860
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461702Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727178
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2759G>A (p.R920K) alteration is located in exon 23 (coding exon 23) of the ITGA10 gene. This alteration results from a G to A substitution at nucleotide position 2759, causing the arginine (R) at amino acid position 920 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