chr4-87845484-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020203.6(MEPE):c.616A>G(p.Ser206Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00336 in 1,613,824 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S206I) has been classified as Likely benign.
Frequency
Consequence
NM_020203.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEPE | NM_020203.6 | c.616A>G | p.Ser206Gly | missense_variant | 4/4 | ENST00000361056.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEPE | ENST00000361056.4 | c.616A>G | p.Ser206Gly | missense_variant | 4/4 | 1 | NM_020203.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00219 AC: 333AN: 152190Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00290 AC: 725AN: 249652Hom.: 4 AF XY: 0.00286 AC XY: 387AN XY: 135112
GnomAD4 exome AF: 0.00348 AC: 5086AN: 1461516Hom.: 20 Cov.: 31 AF XY: 0.00333 AC XY: 2424AN XY: 727092
GnomAD4 genome ? AF: 0.00219 AC: 333AN: 152308Hom.: 1 Cov.: 32 AF XY: 0.00259 AC XY: 193AN XY: 74496
ClinVar
Submissions by phenotype
MEPE-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 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