17-50064095-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002204.4(ITGA3):c.225C>A(p.Pro75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,670 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P75P) has been classified as Likely benign.
Frequency
Consequence
NM_002204.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA3 | NM_002204.4 | c.225C>A | p.Pro75= | synonymous_variant | 2/26 | ENST00000320031.13 | |
ITGA3 | XM_005257308.3 | c.225C>A | p.Pro75= | synonymous_variant | 2/24 | ||
ITGA3 | XM_047435922.1 | c.225C>A | p.Pro75= | synonymous_variant | 2/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA3 | ENST00000320031.13 | c.225C>A | p.Pro75= | synonymous_variant | 2/26 | 1 | NM_002204.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247030Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133974
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460618Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726504
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74276
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at