chr3-15563515-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012260.4(HACL1):c.1547C>T(p.Ser516Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250414Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135296
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459278Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726104
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1547C>T (p.S516L) alteration is located in exon 16 (coding exon 16) of the HACL1 gene. This alteration results from a C to T substitution at nucleotide position 1547, causing the serine (S) at amino acid position 516 to be replaced by a leucine (L). 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