rs143314030
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006620.4(HBS1L):āc.1270A>Gā(p.Lys424Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,573,522 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 (ā ).
Frequency
Consequence
NM_006620.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.1270A>G | p.Lys424Glu | missense_variant | Exon 10 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.1144A>G | p.Lys382Glu | missense_variant | Exon 9 of 17 | NP_001138630.1 | ||
HBS1L | NM_001363686.2 | c.778A>G | p.Lys260Glu | missense_variant | Exon 11 of 19 | NP_001350615.1 | ||
HBS1L | XM_047418093.1 | c.1270A>G | p.Lys424Glu | missense_variant | Exon 10 of 16 | XP_047274049.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000879 AC: 2AN: 227406Hom.: 0 AF XY: 0.00000809 AC XY: 1AN XY: 123594
GnomAD4 exome AF: 0.00000704 AC: 10AN: 1421418Hom.: 0 Cov.: 26 AF XY: 0.00000424 AC XY: 3AN XY: 706770
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1270A>G (p.K424E) alteration is located in exon 10 (coding exon 10) of the HBS1L gene. This alteration results from a A to G substitution at nucleotide position 1270, causing the lysine (K) at amino acid position 424 to be replaced by a glutamic acid (E). 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