4-25862719-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015187.5(SEL1L3):c.118C>A(p.Leu40Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,287,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015187.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEL1L3 | NM_015187.5 | c.118C>A | p.Leu40Ile | missense_variant | 1/24 | ENST00000399878.8 | |
LOC102723733 | XR_427503.5 | n.1027+566G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEL1L3 | ENST00000399878.8 | c.118C>A | p.Leu40Ile | missense_variant | 1/24 | 1 | NM_015187.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151294Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000371 AC: 1AN: 26972Hom.: 0 AF XY: 0.0000621 AC XY: 1AN XY: 16098
GnomAD4 exome AF: 0.0000158 AC: 18AN: 1135892Hom.: 0 Cov.: 30 AF XY: 0.0000145 AC XY: 8AN XY: 549854
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151294Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73860
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at