8-9003110-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_153332.4(ERI1):c.47T>C(p.Leu16Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 1,246,258 control chromosomes in the GnomAD database, including 501,155 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_153332.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERI1 | NM_153332.4 | c.47T>C | p.Leu16Pro | missense_variant | 1/7 | ENST00000250263.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERI1 | ENST00000250263.8 | c.47T>C | p.Leu16Pro | missense_variant | 1/7 | 1 | NM_153332.4 | P1 | |
ERI1 | ENST00000519292.5 | c.47T>C | p.Leu16Pro | missense_variant | 1/8 | 2 | P1 | ||
ERI1 | ENST00000520684.5 | c.47T>C | p.Leu16Pro | missense_variant, NMD_transcript_variant | 1/6 | 5 | |||
ERI1 | ENST00000521844.1 | c.47T>C | p.Leu16Pro | missense_variant, NMD_transcript_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.873 AC: 132825AN: 152168Hom.: 58166 Cov.: 35
GnomAD3 exomes AF: 0.889 AC: 11220AN: 12616Hom.: 5005 AF XY: 0.890 AC XY: 5674AN XY: 6378
GnomAD4 exome AF: 0.899 AC: 984009AN: 1093972Hom.: 442937 Cov.: 54 AF XY: 0.900 AC XY: 465604AN XY: 517396
GnomAD4 genome ? AF: 0.873 AC: 132937AN: 152286Hom.: 58218 Cov.: 35 AF XY: 0.869 AC XY: 64748AN XY: 74474
ClinVar
Submissions by phenotype
ERI1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at