rs12041280
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_021958.4(HLX):c.451G>A(p.Ala151Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 1,613,744 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_021958.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLX | NM_021958.4 | c.451G>A | p.Ala151Thr | missense_variant | 1/4 | ENST00000366903.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLX | ENST00000366903.8 | c.451G>A | p.Ala151Thr | missense_variant | 1/4 | 1 | NM_021958.4 | P1 | |
HLX | ENST00000549319.2 | n.878G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000453 AC: 69AN: 152256Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.000759 AC: 187AN: 246528Hom.: 1 AF XY: 0.000641 AC XY: 86AN XY: 134200
GnomAD4 exome AF: 0.000288 AC: 421AN: 1461370Hom.: 3 Cov.: 33 AF XY: 0.000263 AC XY: 191AN XY: 726956
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152374Hom.: 2 Cov.: 34 AF XY: 0.000510 AC XY: 38AN XY: 74506
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at