17-41725052-C-T
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_177977.3(HAP1):c.1509G>A(p.Thr503Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,612,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_177977.3 synonymous
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251128 AF XY: 0.0000147 show subpopulations
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1460198Hom.: 0 Cov.: 35 AF XY: 0.00000826 AC XY: 6AN XY: 726490 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74310 show subpopulations
ClinVar
Submissions by phenotype
HAP1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at