3-121633119-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005335.6(HCLS1):āc.956C>Gā(p.Thr319Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005335.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCLS1 | NM_005335.6 | c.956C>G | p.Thr319Ser | missense_variant | 11/14 | ENST00000314583.8 | |
HCLS1 | NM_001292041.2 | c.845C>G | p.Thr282Ser | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCLS1 | ENST00000314583.8 | c.956C>G | p.Thr319Ser | missense_variant | 11/14 | 1 | NM_005335.6 | P1 | |
HCLS1 | ENST00000428394.6 | c.845C>G | p.Thr282Ser | missense_variant | 10/13 | 2 | |||
HCLS1 | ENST00000473883.5 | n.1759C>G | non_coding_transcript_exon_variant | 6/9 | 2 | ||||
HCLS1 | ENST00000495491.5 | c.*271C>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461048Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726720
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.