17-75752282-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000213.5(ITGB4):c.3902G>A(p.Arg1301His) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,256 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1301C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000213.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB4 | NM_000213.5 | c.3902G>A | p.Arg1301His | missense_variant | 31/40 | ENST00000200181.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB4 | ENST00000200181.8 | c.3902G>A | p.Arg1301His | missense_variant | 31/40 | 1 | NM_000213.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461026Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726822
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.3902G>A (p.R1301H) alteration is located in exon 31 (coding exon 30) of the ITGB4 gene. This alteration results from a G to A substitution at nucleotide position 3902, causing the arginine (R) at amino acid position 1301 to be replaced by a histidine (H). 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