1-228165893-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010867.4(IBA57):c.77C>T(p.Ala26Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000785 in 1,400,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A26A) has been classified as Likely benign.
Frequency
Consequence
NM_001010867.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152044Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000455 AC: 2AN: 43992Hom.: 0 AF XY: 0.0000754 AC XY: 2AN XY: 26536
GnomAD4 exome AF: 0.00000320 AC: 4AN: 1248454Hom.: 0 Cov.: 30 AF XY: 0.00000327 AC XY: 2AN XY: 611914
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74396
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.77C>T (p.A26V) alteration is located in exon 1 (coding exon 1) of the IBA57 gene. This alteration results from a C to T substitution at nucleotide position 77, causing the alanine (A) at amino acid position 26 to be replaced by a valine (V). 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