chr1-169728076-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000333360.12(SELE):āc.1261G>Cā(p.Glu421Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,612,824 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000333360.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELE | NM_000450.2 | c.1261G>C | p.Glu421Gln | missense_variant | 8/14 | ENST00000333360.12 | NP_000441.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELE | ENST00000333360.12 | c.1261G>C | p.Glu421Gln | missense_variant | 8/14 | 1 | NM_000450.2 | ENSP00000331736 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0125 AC: 1905AN: 152202Hom.: 36 Cov.: 33
GnomAD3 exomes AF: 0.00324 AC: 809AN: 249322Hom.: 12 AF XY: 0.00235 AC XY: 316AN XY: 134702
GnomAD4 exome AF: 0.00134 AC: 1963AN: 1460504Hom.: 47 Cov.: 32 AF XY: 0.00111 AC XY: 804AN XY: 726498
GnomAD4 genome AF: 0.0126 AC: 1920AN: 152320Hom.: 36 Cov.: 33 AF XY: 0.0122 AC XY: 907AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at