3-15560879-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.1723C>T(p.Arg575Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,606,514 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 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: 0.000138 AC: 21AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249780Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135050
GnomAD4 exome AF: 0.00000963 AC: 14AN: 1454368Hom.: 0 Cov.: 27 AF XY: 0.0000110 AC XY: 8AN XY: 724076
GnomAD4 genome AF: 0.000138 AC: 21AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1723C>T (p.R575C) alteration is located in exon 17 (coding exon 17) of the HACL1 gene. This alteration results from a C to T substitution at nucleotide position 1723, causing the arginine (R) at amino acid position 575 to be replaced by a cysteine (C). 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