chr13-42888372-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000313640.11(EPSTI1):c.1111C>T(p.Leu371Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPSTI1 | NM_033255.5 | c.*122C>T | 3_prime_UTR_variant | 11/11 | ENST00000313624.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPSTI1 | ENST00000313640.11 | c.1111C>T | p.Leu371Phe | missense_variant | 13/13 | 1 | |||
EPSTI1 | ENST00000313624.12 | c.*122C>T | 3_prime_UTR_variant | 11/11 | 1 | NM_033255.5 | P4 | ||
EPSTI1 | ENST00000540470.5 | n.2619C>T | non_coding_transcript_exon_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251414Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135878
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461858Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727226
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.1111C>T (p.L371F) alteration is located in exon 13 (coding exon 13) of the EPSTI1 gene. This alteration results from a C to T substitution at nucleotide position 1111, causing the leucine (L) at amino acid position 371 to be replaced by a phenylalanine (F). 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