18-12984145-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001013437.2(SEH1L):c.1025C>A(p.Thr342Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,612,740 control chromosomes in the GnomAD database, including 340,975 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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
NM_001013437.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEH1L | NM_001013437.2 | c.1025C>A | p.Thr342Asn | missense_variant | 8/9 | ENST00000399892.7 | NP_001013455.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEH1L | ENST00000399892.7 | c.1025C>A | p.Thr342Asn | missense_variant | 8/9 | 1 | NM_001013437.2 | ENSP00000382779 | P3 | |
SEH1L | ENST00000262124.15 | c.1025C>A | p.Thr342Asn | missense_variant | 8/9 | 1 | ENSP00000262124 | A1 | ||
SEH1L | ENST00000590843.1 | n.2869C>A | non_coding_transcript_exon_variant | 3/4 | 1 | |||||
SEH1L | ENST00000592582.5 | n.3548C>A | non_coding_transcript_exon_variant | 5/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.719 AC: 109436AN: 152108Hom.: 40877 Cov.: 34
GnomAD3 exomes AF: 0.671 AC: 168518AN: 251240Hom.: 57664 AF XY: 0.670 AC XY: 90938AN XY: 135816
GnomAD4 exome AF: 0.636 AC: 929302AN: 1460514Hom.: 300036 Cov.: 42 AF XY: 0.638 AC XY: 463843AN XY: 726614
GnomAD4 genome AF: 0.720 AC: 109553AN: 152226Hom.: 40939 Cov.: 34 AF XY: 0.720 AC XY: 53601AN XY: 74422
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at