13-42888392-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000313640.11(EPSTI1):c.1091T>C(p.Leu364Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000313640.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPSTI1 | NM_033255.5 | c.*102T>C | 3_prime_UTR_variant | 11/11 | ENST00000313624.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPSTI1 | ENST00000313640.11 | c.1091T>C | p.Leu364Ser | missense_variant | 13/13 | 1 | |||
EPSTI1 | ENST00000313624.12 | c.*102T>C | 3_prime_UTR_variant | 11/11 | 1 | NM_033255.5 | P4 | ||
EPSTI1 | ENST00000540470.5 | n.2599T>C | non_coding_transcript_exon_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251408Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135868
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461866Hom.: 0 Cov.: 33 AF XY: 0.0000536 AC XY: 39AN XY: 727230
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.1091T>C (p.L364S) alteration is located in exon 13 (coding exon 13) of the EPSTI1 gene. This alteration results from a T to C substitution at nucleotide position 1091, causing the leucine (L) at amino acid position 364 to be replaced by a serine (S). 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