chr19-13765090-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001031727.4(MRI1):c.352G>A(p.Glu118Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,540,396 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001031727.4 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 |
---|---|---|---|---|---|---|---|
MRI1 | NM_001031727.4 | c.352G>A | p.Glu118Lys | missense_variant | 2/6 | ENST00000040663.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRI1 | ENST00000040663.8 | c.352G>A | p.Glu118Lys | missense_variant | 2/6 | 1 | NM_001031727.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00142 AC: 216AN: 152242Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00105 AC: 171AN: 162836Hom.: 0 AF XY: 0.00113 AC XY: 101AN XY: 89364
GnomAD4 exome AF: 0.00224 AC: 3111AN: 1388036Hom.: 4 Cov.: 32 AF XY: 0.00216 AC XY: 1484AN XY: 687222
GnomAD4 genome ? AF: 0.00142 AC: 216AN: 152360Hom.: 0 Cov.: 31 AF XY: 0.00130 AC XY: 97AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at