3-15563368-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012260.4(HACL1):c.1694G>A(p.Arg565Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000493 in 1,611,716 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000288 AC: 72AN: 250328Hom.: 0 AF XY: 0.000333 AC XY: 45AN XY: 135282
GnomAD4 exome AF: 0.000512 AC: 748AN: 1459640Hom.: 1 Cov.: 30 AF XY: 0.000492 AC XY: 357AN XY: 726218
GnomAD4 genome AF: 0.000302 AC: 46AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1694G>A (p.R565Q) alteration is located in exon 16 (coding exon 16) of the HACL1 gene. This alteration results from a G to A substitution at nucleotide position 1694, causing the arginine (R) at amino acid position 565 to be replaced by a glutamine (Q). 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