chr1-36322547-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001304762.2(EVA1B):āc.246G>Cā(p.Glu82Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,597,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001304762.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVA1B | NM_001304762.2 | c.246G>C | p.Glu82Asp | missense_variant | 3/3 | ENST00000490466.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVA1B | ENST00000490466.2 | c.246G>C | p.Glu82Asp | missense_variant | 3/3 | 2 | NM_001304762.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000465 AC: 10AN: 215116Hom.: 0 AF XY: 0.0000336 AC XY: 4AN XY: 119174
GnomAD4 exome AF: 0.000146 AC: 211AN: 1445308Hom.: 0 Cov.: 36 AF XY: 0.000138 AC XY: 99AN XY: 718926
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 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