chr15-68335825-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001004439.2(ITGA11):c.1297G>A(p.Val433Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 1,612,980 control chromosomes in the GnomAD database, including 5,339 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001004439.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGA11 | NM_001004439.2 | c.1297G>A | p.Val433Met | missense_variant | 12/30 | ENST00000315757.9 | NP_001004439.1 | |
ITGA11 | XM_011521363.3 | c.1090G>A | p.Val364Met | missense_variant | 10/28 | XP_011519665.1 | ||
ITGA11 | XM_005254228.4 | c.991G>A | p.Val331Met | missense_variant | 10/28 | XP_005254285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA11 | ENST00000315757.9 | c.1297G>A | p.Val433Met | missense_variant | 12/30 | 1 | NM_001004439.2 | ENSP00000327290.7 | ||
ITGA11 | ENST00000423218.6 | c.1297G>A | p.Val433Met | missense_variant | 12/30 | 2 | ENSP00000403392.2 | |||
ITGA11 | ENST00000569346.5 | n.276G>A | non_coding_transcript_exon_variant | 1/4 | 4 | |||||
ITGA11 | ENST00000566429.1 | n.197-11G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0583 AC: 8881AN: 152212Hom.: 339 Cov.: 33
GnomAD3 exomes AF: 0.0664 AC: 16351AN: 246158Hom.: 683 AF XY: 0.0679 AC XY: 9089AN XY: 133850
GnomAD4 exome AF: 0.0803 AC: 117314AN: 1460650Hom.: 5000 Cov.: 34 AF XY: 0.0796 AC XY: 57841AN XY: 726526
GnomAD4 genome AF: 0.0584 AC: 8889AN: 152330Hom.: 339 Cov.: 33 AF XY: 0.0571 AC XY: 4252AN XY: 74490
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at