rs2854741
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000433992.2(CYP2D7):c.989G>T(p.Arg330Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 152,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000433992.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2D7 | NR_002570.6 | n.1006-55G>T | intron_variant, non_coding_transcript_variant | ||||
CYP2D7 | NR_145674.3 | n.1008G>T | splice_region_variant, non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2D7 | ENST00000433992.2 | c.989G>T | p.Arg330Met | missense_variant, splice_region_variant | 7/9 | 1 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152038Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000142 AC: 2AN: 1407394Hom.: 0 Cov.: 25 AF XY: 0.00000285 AC XY: 2AN XY: 701642
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74242
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at