rs200327611
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006620.4(HBS1L):c.452C>T(p.Thr151Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000465 in 1,612,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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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.452C>T | p.Thr151Ile | missense_variant | Exon 5 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.326C>T | p.Thr109Ile | missense_variant | Exon 4 of 17 | NP_001138630.1 | ||
HBS1L | XM_047418093.1 | c.452C>T | p.Thr151Ile | missense_variant | Exon 5 of 16 | XP_047274049.1 | ||
HBS1L | NM_001363686.2 | c.-41C>T | 5_prime_UTR_variant | Exon 6 of 19 | NP_001350615.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000270 AC: 41AN: 152108Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251056Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135672
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460116Hom.: 0 Cov.: 30 AF XY: 0.0000262 AC XY: 19AN XY: 726472
GnomAD4 genome AF: 0.000269 AC: 41AN: 152226Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.452C>T (p.T151I) alteration is located in exon 5 (coding exon 5) of the HBS1L gene. This alteration results from a C to T substitution at nucleotide position 452, causing the threonine (T) at amino acid position 151 to be replaced by an isoleucine (I). 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