rs1774318038
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006620.4(HBS1L):c.1921G>A(p.Ala641Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000251 in 1,596,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006620.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.1921G>A | p.Ala641Thr | missense_variant | Exon 17 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.1795G>A | p.Ala599Thr | missense_variant | Exon 16 of 17 | NP_001138630.1 | ||
HBS1L | NM_001363686.2 | c.1429G>A | p.Ala477Thr | missense_variant | Exon 18 of 19 | NP_001350615.1 | ||
HBS1L | XM_047418093.1 | c.*11G>A | 3_prime_UTR_variant | Exon 16 of 16 | XP_047274049.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151872Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1444416Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 717826
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151872Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74142
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1921G>A (p.A641T) alteration is located in exon 17 (coding exon 17) of the HBS1L gene. This alteration results from a G to A substitution at nucleotide position 1921, causing the alanine (A) at amino acid position 641 to be replaced by a threonine (T). 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