rs757660
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012429.5(SEC14L2):c.32G>A(p.Arg11Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,544,374 control chromosomes in the GnomAD database, including 80,072 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_012429.5 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 | UniProt |
---|---|---|---|---|---|---|---|
SEC14L2 | NM_012429.5 | c.32G>A | p.Arg11Lys | missense_variant | 1/12 | ENST00000615189.5 | |
SEC14L2 | NM_033382.3 | c.32G>A | p.Arg11Lys | missense_variant | 1/11 | ||
SEC14L2 | NM_001204204.3 | c.32G>A | p.Arg11Lys | missense_variant | 1/10 | ||
SEC14L2 | NM_001291932.2 | c.-55G>A | 5_prime_UTR_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC14L2 | ENST00000615189.5 | c.32G>A | p.Arg11Lys | missense_variant | 1/12 | 1 | NM_012429.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.348 AC: 52675AN: 151420Hom.: 9428 Cov.: 31
GnomAD3 exomes AF: 0.337 AC: 49563AN: 147020Hom.: 8638 AF XY: 0.337 AC XY: 26379AN XY: 78256
GnomAD4 exome AF: 0.315 AC: 439203AN: 1392836Hom.: 70630 Cov.: 36 AF XY: 0.317 AC XY: 217877AN XY: 686992
GnomAD4 genome ? AF: 0.348 AC: 52731AN: 151538Hom.: 9442 Cov.: 31 AF XY: 0.354 AC XY: 26246AN XY: 74076
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at