chr3-15567912-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_012260.4(HACL1):āc.1341A>Gā(p.Gln447Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,614,120 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_012260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000310 AC: 78AN: 251418Hom.: 0 AF XY: 0.000331 AC XY: 45AN XY: 135880
GnomAD4 exome AF: 0.000147 AC: 215AN: 1461764Hom.: 1 Cov.: 31 AF XY: 0.000155 AC XY: 113AN XY: 727194
GnomAD4 genome AF: 0.000131 AC: 20AN: 152356Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74512
ClinVar
Submissions by phenotype
HACL1-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