5-52933895-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_181501.2(ITGA1):c.2863T>C(p.Ser955Pro) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000552 in 1,450,538 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181501.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151842Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000514 AC: 1AN: 194624Hom.: 0 AF XY: 0.00000933 AC XY: 1AN XY: 107162
GnomAD4 exome AF: 0.00000539 AC: 7AN: 1298578Hom.: 0 Cov.: 19 AF XY: 0.00000309 AC XY: 2AN XY: 646416
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151960Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2863T>C (p.S955P) alteration is located in exon 23 (coding exon 23) of the ITGA1 gene. This alteration results from a T to C substitution at nucleotide position 2863, causing the serine (S) at amino acid position 955 to be replaced by a proline (P). 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