chr13-42888292-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
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. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000313640.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPSTI1 | NM_033255.5 | c.*202A>G | 3_prime_UTR_variant | 11/11 | ENST00000313624.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPSTI1 | ENST00000313640.11 | c.1191A>G | p.Ile397Met | missense_variant | 13/13 | 1 | |||
EPSTI1 | ENST00000313624.12 | c.*202A>G | 3_prime_UTR_variant | 11/11 | 1 | NM_033255.5 | P4 | ||
EPSTI1 | ENST00000540470.5 | n.2699A>G | non_coding_transcript_exon_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000374 AC: 56AN: 149588Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000180 AC: 45AN: 249780Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135042
GnomAD4 exome AF: 0.0000509 AC: 74AN: 1455224Hom.: 2 Cov.: 33 AF XY: 0.0000428 AC XY: 31AN XY: 723648
GnomAD4 genome ? AF: 0.000374 AC: 56AN: 149684Hom.: 1 Cov.: 32 AF XY: 0.000465 AC XY: 34AN XY: 73140
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | 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