2-97194844-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001354587.1(ANKRD36):c.2479-1G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000594 in 1,591,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_001354587.1 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD36 | NM_001354587.1 | c.2479-1G>A | splice_acceptor_variant, intron_variant | Intron 39 of 75 | ENST00000420699.9 | NP_001341516.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD36 | ENST00000420699.9 | c.2479-1G>A | splice_acceptor_variant, intron_variant | Intron 39 of 75 | 5 | NM_001354587.1 | ENSP00000391950.4 | |||
ANKRD36 | ENST00000461153.7 | c.2479-1G>A | splice_acceptor_variant, intron_variant | Intron 39 of 74 | 5 | ENSP00000419530.3 | ||||
ANKRD36 | ENST00000652721.1 | c.2479-1G>A | splice_acceptor_variant, intron_variant | Intron 39 of 75 | ENSP00000498611.1 |
Frequencies
GnomAD3 genomes AF: 0.000744 AC: 113AN: 151920Hom.: 0 Cov.: 45
GnomAD3 exomes AF: 0.00118 AC: 258AN: 218424Hom.: 0 AF XY: 0.00112 AC XY: 133AN XY: 118696
GnomAD4 exome AF: 0.000579 AC: 834AN: 1439462Hom.: 0 Cov.: 38 AF XY: 0.000589 AC XY: 421AN XY: 715168
GnomAD4 genome AF: 0.000737 AC: 112AN: 152038Hom.: 0 Cov.: 45 AF XY: 0.000632 AC XY: 47AN XY: 74314
ClinVar
Submissions by phenotype
Hearing loss, autosomal recessive Pathogenic:1
Recessive, compound heterozygous with NM_001354587.1: 2589T>G; congenital, moderate-severe progressive SNHL -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at