chr3-124773748-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002213.5(ITGB5):c.1858G>A(p.Ala620Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,492 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002213.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGB5 | ENST00000296181.9 | c.1858G>A | p.Ala620Thr | missense_variant | Exon 11 of 15 | 1 | NM_002213.5 | ENSP00000296181.4 | ||
ITGB5 | ENST00000481591.5 | c.925G>A | p.Ala309Thr | missense_variant | Exon 5 of 7 | 5 | ENSP00000420814.1 | |||
ITGB5 | ENST00000461306.1 | n.197G>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 4 | |||||
ITGB5 | ENST00000488466.5 | c.*71G>A | downstream_gene_variant | 5 | ENSP00000477446.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251348Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135870
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460492Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726576
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1858G>A (p.A620T) alteration is located in exon 11 (coding exon 11) of the ITGB5 gene. This alteration results from a G to A substitution at nucleotide position 1858, causing the alanine (A) at amino acid position 620 to be replaced by a threonine (T). 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