rs12141189
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000366903.8(HLX):āc.346T>Cā(p.Ser116Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 1,612,368 control chromosomes in the GnomAD database, including 47,317 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000366903.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HLX | NM_021958.4 | c.346T>C | p.Ser116Pro | missense_variant | 1/4 | ENST00000366903.8 | NP_068777.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HLX | ENST00000366903.8 | c.346T>C | p.Ser116Pro | missense_variant | 1/4 | 1 | NM_021958.4 | ENSP00000355870 | P1 | |
HLX | ENST00000549319.2 | n.773T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.230 AC: 34929AN: 151988Hom.: 4153 Cov.: 33
GnomAD3 exomes AF: 0.244 AC: 59203AN: 242226Hom.: 7632 AF XY: 0.238 AC XY: 31515AN XY: 132336
GnomAD4 exome AF: 0.240 AC: 350889AN: 1460262Hom.: 43156 Cov.: 35 AF XY: 0.238 AC XY: 172835AN XY: 726452
GnomAD4 genome AF: 0.230 AC: 34958AN: 152106Hom.: 4161 Cov.: 33 AF XY: 0.234 AC XY: 17369AN XY: 74358
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at