10-32272041-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001272004.3(EPC1):c.1990G>A(p.Val664Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000825 in 1,612,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001272004.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPC1 | NM_001272004.3 | c.1990G>A | p.Val664Ile | missense_variant | 12/14 | ENST00000319778.11 | NP_001258933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPC1 | ENST00000319778.11 | c.1990G>A | p.Val664Ile | missense_variant | 12/14 | 1 | NM_001272004.3 | ENSP00000318559.6 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 248982Hom.: 0 AF XY: 0.0000965 AC XY: 13AN XY: 134694
GnomAD4 exome AF: 0.0000637 AC: 93AN: 1460402Hom.: 0 Cov.: 32 AF XY: 0.0000688 AC XY: 50AN XY: 726436
GnomAD4 genome AF: 0.000263 AC: 40AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 10, 2024 | The c.2059G>A (p.V687I) alteration is located in exon 13 (coding exon 13) of the EPC1 gene. This alteration results from a G to A substitution at nucleotide position 2059, causing the valine (V) at amino acid position 687 to be replaced by an isoleucine (I). 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