13-42888292-T-C
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000313640.11(EPSTI1):c.1191A>G(p.Ile397Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000081 in 1,604,908 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I397T) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000313640.11 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPSTI1 | ENST00000313640.11 | c.1191A>G | p.Ile397Met | missense_variant | Exon 13 of 13 | 1 | ENSP00000318982.7 | |||
EPSTI1 | ENST00000313624.12 | c.*202A>G | 3_prime_UTR_variant | Exon 11 of 11 | 1 | NM_033255.5 | ENSP00000318643.7 | |||
EPSTI1 | ENST00000540470.5 | n.2699A>G | non_coding_transcript_exon_variant | Exon 11 of 11 | 2 | |||||
EPSTI1 | ENST00000398762.7 | c.*202A>G | downstream_gene_variant | 5 | ENSP00000381746.3 |
Frequencies
GnomAD3 genomes AF: 0.000374 AC: 56AN: 149588Hom.: 1 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000180 AC: 45AN: 249780 AF XY: 0.000148 show subpopulations
GnomAD4 exome AF: 0.0000509 AC: 74AN: 1455224Hom.: 2 Cov.: 33 AF XY: 0.0000428 AC XY: 31AN XY: 723648 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000374 AC: 56AN: 149684Hom.: 1 Cov.: 32 AF XY: 0.000465 AC XY: 34AN XY: 73140 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at