4-25776286-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015187.5(SEL1L3):c.2660A>C(p.Glu887Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000993 in 1,611,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEL1L3 | ENST00000399878.8 | c.2660A>C | p.Glu887Ala | missense_variant | Exon 17 of 24 | 1 | NM_015187.5 | ENSP00000382767.3 | ||
SEL1L3 | ENST00000264868.9 | c.2555A>C | p.Glu852Ala | missense_variant | Exon 17 of 24 | 1 | ENSP00000264868.5 | |||
SEL1L3 | ENST00000502949.5 | c.2201A>C | p.Glu734Ala | missense_variant | Exon 17 of 24 | 2 | ENSP00000425438.1 | |||
SEL1L3 | ENST00000509290.1 | n.434A>C | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248374Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134796
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1458970Hom.: 0 Cov.: 29 AF XY: 0.00000827 AC XY: 6AN XY: 725934
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2660A>C (p.E887A) alteration is located in exon 17 (coding exon 17) of the SEL1L3 gene. This alteration results from a A to C substitution at nucleotide position 2660, causing the glutamic acid (E) at amino acid position 887 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at