12-54399910-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002205.5(ITGA5):c.2681G>A(p.Arg894Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,614,018 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_002205.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGA5 | NM_002205.5 | c.2681G>A | p.Arg894Gln | missense_variant | Exon 26 of 30 | ENST00000293379.9 | NP_002196.4 | |
ITGA5 | XM_024448970.2 | c.1169G>A | p.Arg390Gln | missense_variant | Exon 13 of 17 | XP_024304738.1 | ||
GPR84-AS1 | NR_120486.1 | n.207-7487C>T | intron_variant | Intron 1 of 3 | ||||
GPR84-AS1 | NR_120487.1 | n.207-7487C>T | intron_variant | Intron 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251446Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135896
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727234
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2681G>A (p.R894Q) alteration is located in exon 26 (coding exon 26) of the ITGA5 gene. This alteration results from a G to A substitution at nucleotide position 2681, causing the arginine (R) at amino acid position 894 to be replaced by a glutamine (Q). 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