chr3-121631920-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005335.6(HCLS1):c.1387G>A(p.Glu463Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005335.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCLS1 | ENST00000314583.8 | c.1387G>A | p.Glu463Lys | missense_variant | Exon 14 of 14 | 1 | NM_005335.6 | ENSP00000320176.3 | ||
HCLS1 | ENST00000428394.6 | c.1276G>A | p.Glu426Lys | missense_variant | Exon 13 of 13 | 2 | ENSP00000387645.2 | |||
HCLS1 | ENST00000473883.5 | n.2190G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251278Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135800
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461854Hom.: 0 Cov.: 33 AF XY: 0.0000468 AC XY: 34AN XY: 727222
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1387G>A (p.E463K) alteration is located in exon 14 (coding exon 13) of the HCLS1 gene. This alteration results from a G to A substitution at nucleotide position 1387, causing the glutamic acid (E) at amino acid position 463 to be replaced by a lysine (K). 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