rs566791217
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006620.4(HBS1L):c.1697G>A(p.Cys566Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000526 in 1,595,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006620.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.1697G>A | p.Cys566Tyr | missense_variant | Exon 15 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.1571G>A | p.Cys524Tyr | missense_variant | Exon 14 of 17 | NP_001138630.1 | ||
HBS1L | NM_001363686.2 | c.1205G>A | p.Cys402Tyr | missense_variant | Exon 16 of 19 | NP_001350615.1 | ||
HBS1L | XM_047418093.1 | c.1697G>A | p.Cys566Tyr | missense_variant | Exon 15 of 16 | XP_047274049.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151890Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000110 AC: 27AN: 244816Hom.: 0 AF XY: 0.000174 AC XY: 23AN XY: 132412
GnomAD4 exome AF: 0.0000561 AC: 81AN: 1443506Hom.: 0 Cov.: 27 AF XY: 0.0000849 AC XY: 61AN XY: 718540
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1697G>A (p.C566Y) alteration is located in exon 15 (coding exon 15) of the HBS1L gene. This alteration results from a G to A substitution at nucleotide position 1697, causing the cysteine (C) at amino acid position 566 to be replaced by a tyrosine (Y). 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