chr1-109757069-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_133181.4(EPS8L3):c.1066C>T(p.Pro356Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 1,613,934 control chromosomes in the GnomAD database, including 8,986 homozygotes. In-silico tool predicts 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_133181.4 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 |
---|---|---|---|---|---|---|---|
EPS8L3 | NM_133181.4 | c.1066C>T | p.Pro356Ser | missense_variant | 12/19 | ENST00000361965.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPS8L3 | ENST00000361965.9 | c.1066C>T | p.Pro356Ser | missense_variant | 12/19 | 1 | NM_133181.4 | P4 | |
ENST00000431955.1 | n.628-18003G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.151 AC: 23009AN: 152014Hom.: 3230 Cov.: 32
GnomAD3 exomes AF: 0.0936 AC: 23531AN: 251378Hom.: 2063 AF XY: 0.0858 AC XY: 11650AN XY: 135854
GnomAD4 exome AF: 0.0709 AC: 103587AN: 1461802Hom.: 5753 Cov.: 32 AF XY: 0.0699 AC XY: 50842AN XY: 727202
GnomAD4 genome AF: 0.151 AC: 23035AN: 152132Hom.: 3233 Cov.: 32 AF XY: 0.149 AC XY: 11065AN XY: 74400
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at