chr3-37471115-C-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_002207.3(ITGA9):c.294C>A(p.Thr98Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00522 in 1,613,906 control chromosomes in the GnomAD database, including 274 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002207.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA9 | ENST00000264741.10 | c.294C>A | p.Thr98Thr | synonymous_variant | Exon 2 of 28 | 1 | NM_002207.3 | ENSP00000264741.5 | ||
ITGA9 | ENST00000422441.5 | c.294C>A | p.Thr98Thr | synonymous_variant | Exon 2 of 16 | 1 | ENSP00000397258.1 |
Frequencies
GnomAD3 genomes AF: 0.0248 AC: 3771AN: 151996Hom.: 145 Cov.: 31
GnomAD3 exomes AF: 0.00736 AC: 1852AN: 251470Hom.: 58 AF XY: 0.00578 AC XY: 785AN XY: 135914
GnomAD4 exome AF: 0.00318 AC: 4653AN: 1461792Hom.: 128 Cov.: 31 AF XY: 0.00286 AC XY: 2082AN XY: 727194
GnomAD4 genome AF: 0.0248 AC: 3769AN: 152114Hom.: 146 Cov.: 31 AF XY: 0.0236 AC XY: 1757AN XY: 74350
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
ITGA9-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at