chr19-13766049-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001031727.4(MRI1):c.467C>T(p.Ala156Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000732 in 1,612,890 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Uncertain significance (★).
Frequency
Consequence
NM_001031727.4 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 |
---|---|---|---|---|---|---|---|
MRI1 | NM_001031727.4 | c.467C>T | p.Ala156Val | missense_variant | 3/6 | ENST00000040663.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRI1 | ENST00000040663.8 | c.467C>T | p.Ala156Val | missense_variant | 3/6 | 1 | NM_001031727.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000168 AC: 42AN: 249570Hom.: 1 AF XY: 0.000214 AC XY: 29AN XY: 135240
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1460610Hom.: 2 Cov.: 31 AF XY: 0.000120 AC XY: 87AN XY: 726608
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152280Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.467C>T (p.A156V) alteration is located in exon 3 (coding exon 3) of the MRI1 gene. This alteration results from a C to T substitution at nucleotide position 467, causing the alanine (A) at amino acid position 156 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at