18-63960198-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001123366.2(HMSD):āc.263T>Cā(p.Ile88Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001123366.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMSD | NM_001123366.2 | c.263T>C | p.Ile88Thr | missense_variant | 4/4 | ENST00000408945.5 | NP_001116838.1 | |
HMSD | XM_017025710.2 | c.263T>C | p.Ile88Thr | missense_variant | 4/5 | XP_016881199.1 | ||
HMSD | XM_011525930.3 | c.263T>C | p.Ile88Thr | missense_variant | 4/5 | XP_011524232.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HMSD | ENST00000408945.5 | c.263T>C | p.Ile88Thr | missense_variant | 4/4 | 3 | NM_001123366.2 | ENSP00000386207.3 | ||
HMSD | ENST00000526932.1 | c.160T>C | p.Ter54Glnext*? | stop_lost, splice_region_variant | 2/2 | 3 | ENSP00000431632.1 | |||
HMSD | ENST00000481726.1 | n.235T>C | non_coding_transcript_exon_variant | 3/6 | 5 | |||||
HMSD | ENST00000498680.1 | n.17T>C | non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460440Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726320
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.263T>C (p.I88T) alteration is located in exon 4 (coding exon 3) of the HMSD gene. This alteration results from a T to C substitution at nucleotide position 263, causing the isoleucine (I) at amino acid position 88 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
Publications
No publications associated with this variant yet.