chr5-150407313-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001025159.3(CD74):c.137G>T(p.Arg46Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,607,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001025159.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151854Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000211 AC: 5AN: 237298Hom.: 0 AF XY: 0.0000233 AC XY: 3AN XY: 128550
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1455880Hom.: 0 Cov.: 31 AF XY: 0.00000691 AC XY: 5AN XY: 723772
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151854Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74132
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at