3-124796776-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002213.5(ITGB5):āc.1305C>Gā(p.Ser435Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000067 in 1,612,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002213.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGB5 | NM_002213.5 | c.1305C>G | p.Ser435Arg | missense_variant | 10/15 | ENST00000296181.9 | NP_002204.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGB5 | ENST00000296181.9 | c.1305C>G | p.Ser435Arg | missense_variant | 10/15 | 1 | NM_002213.5 | ENSP00000296181 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000101 AC: 25AN: 248454Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134420
GnomAD4 exome AF: 0.0000336 AC: 49AN: 1460212Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21AN XY: 726138
GnomAD4 genome AF: 0.000387 AC: 59AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.1305C>G (p.S435R) alteration is located in exon 10 (coding exon 10) of the ITGB5 gene. This alteration results from a C to G substitution at nucleotide position 1305, causing the serine (S) at amino acid position 435 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