chr5-52849373-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181501.2(ITGA1):c.70C>T(p.Arg24Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,606,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181501.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA1 | NM_181501.2 | c.70C>T | p.Arg24Cys | missense_variant | 2/29 | ENST00000282588.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA1 | ENST00000282588.7 | c.70C>T | p.Arg24Cys | missense_variant | 2/29 | 1 | NM_181501.2 | P1 | |
ITGA1 | ENST00000650673.1 | c.70C>T | p.Arg24Cys | missense_variant, NMD_transcript_variant | 2/29 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250678Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135498
GnomAD4 exome AF: 0.0000131 AC: 19AN: 1454090Hom.: 0 Cov.: 29 AF XY: 0.0000111 AC XY: 8AN XY: 723284
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | The c.70C>T (p.R24C) alteration is located in exon 2 (coding exon 2) of the ITGA1 gene. This alteration results from a C to T substitution at nucleotide position 70, causing the arginine (R) at amino acid position 24 to be replaced by a cysteine (C). 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