10-32907089-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_033668.2(ITGB1):c.2386G>A(p.Gly796Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000603 in 1,359,486 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033668.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGB1 | NM_002211.4 | c.2331+1279G>A | intron_variant | Intron 15 of 15 | ENST00000302278.8 | NP_002202.2 | ||
ITGB1 | NM_033668.2 | c.2386G>A | p.Gly796Arg | missense_variant | Exon 15 of 16 | NP_391988.1 | ||
ITGB1 | NM_133376.3 | c.2331+1279G>A | intron_variant | Intron 15 of 15 | NP_596867.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 151944Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000648 AC: 16AN: 247076Hom.: 0 AF XY: 0.0000751 AC XY: 10AN XY: 133216
GnomAD4 exome AF: 0.0000513 AC: 62AN: 1207542Hom.: 0 Cov.: 26 AF XY: 0.0000535 AC XY: 32AN XY: 598438
GnomAD4 genome AF: 0.000132 AC: 20AN: 151944Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74200
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2386G>A (p.G796R) alteration is located in exon 15 (coding exon 15) of the ITGB1 gene. This alteration results from a G to A substitution at nucleotide position 2386, causing the glycine (G) at amino acid position 796 to be replaced by an arginine (R). 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