chr1-42830899-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001017922.2(ERMAP):c.217C>T(p.Arg73Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000498 in 1,613,940 control chromosomes in the GnomAD database, including 3 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R73H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001017922.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERMAP | NM_001017922.2 | c.217C>T | p.Arg73Cys | missense_variant | 4/12 | ENST00000372517.8 | NP_001017922.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00272 AC: 414AN: 152124Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000614 AC: 154AN: 250812Hom.: 0 AF XY: 0.000361 AC XY: 49AN XY: 135588
GnomAD4 exome AF: 0.000265 AC: 388AN: 1461698Hom.: 0 Cov.: 32 AF XY: 0.000221 AC XY: 161AN XY: 727152
GnomAD4 genome AF: 0.00273 AC: 415AN: 152242Hom.: 3 Cov.: 32 AF XY: 0.00231 AC XY: 172AN XY: 74452
ClinVar
Submissions by phenotype
ERMAP-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 01, 2021 | 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