6-134982485-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_006620.4(HBS1L):c.1570C>T(p.Pro524Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,607,382 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.1570C>T | p.Pro524Ser | missense_variant | Exon 13 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.1444C>T | p.Pro482Ser | missense_variant | Exon 12 of 17 | NP_001138630.1 | ||
HBS1L | NM_001363686.2 | c.1078C>T | p.Pro360Ser | missense_variant | Exon 14 of 19 | NP_001350615.1 | ||
HBS1L | XM_047418093.1 | c.1570C>T | p.Pro524Ser | missense_variant | Exon 13 of 16 | XP_047274049.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152028Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455354Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 724398
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1570C>T (p.P524S) alteration is located in exon 13 (coding exon 13) of the HBS1L gene. This alteration results from a C to T substitution at nucleotide position 1570, causing the proline (P) at amino acid position 524 to be replaced by a serine (S). 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