chr6-106099497-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001198.4(PRDM1):c.609C>G(p.Asp203Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,613,910 control chromosomes in the GnomAD database, including 23,745 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001198.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM1 | NM_001198.4 | c.609C>G | p.Asp203Glu | missense_variant | 4/7 | ENST00000369096.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM1 | ENST00000369096.9 | c.609C>G | p.Asp203Glu | missense_variant | 4/7 | 1 | NM_001198.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25171AN: 152046Hom.: 2223 Cov.: 32
GnomAD3 exomes AF: 0.162 AC: 40749AN: 251394Hom.: 3530 AF XY: 0.165 AC XY: 22454AN XY: 135880
GnomAD4 exome AF: 0.168 AC: 245708AN: 1461746Hom.: 21525 Cov.: 33 AF XY: 0.169 AC XY: 122681AN XY: 727178
GnomAD4 genome ? AF: 0.165 AC: 25176AN: 152164Hom.: 2220 Cov.: 32 AF XY: 0.169 AC XY: 12536AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 18, 2020 | This variant is associated with the following publications: (PMID: 21085059) - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at