chr6-134978710-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006620.4(HBS1L):āc.1766A>Gā(p.Asn589Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000437 in 1,602,676 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.1766A>G | p.Asn589Ser | missense_variant | Exon 15 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.1640A>G | p.Asn547Ser | missense_variant | Exon 14 of 17 | NP_001138630.1 | ||
HBS1L | NM_001363686.2 | c.1274A>G | p.Asn425Ser | missense_variant | Exon 16 of 19 | NP_001350615.1 | ||
HBS1L | XM_047418093.1 | c.1766A>G | p.Asn589Ser | missense_variant | Exon 15 of 16 | XP_047274049.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247220Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133756
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450714Hom.: 0 Cov.: 28 AF XY: 0.00000416 AC XY: 3AN XY: 721860
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1766A>G (p.N589S) alteration is located in exon 15 (coding exon 15) of the HBS1L gene. This alteration results from a A to G substitution at nucleotide position 1766, causing the asparagine (N) at amino acid position 589 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