NM_001393986.1:c.3070T>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001393986.1(PRDM2):c.3070T>A(p.Ser1024Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0413 in 1,610,400 control chromosomes in the GnomAD database, including 1,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001393986.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRDM2 | NM_001393986.1 | c.3070T>A | p.Ser1024Thr | missense_variant | Exon 8 of 10 | ENST00000311066.10 | NP_001380915.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0313 AC: 4708AN: 150640Hom.: 116 Cov.: 30
GnomAD3 exomes AF: 0.0346 AC: 8686AN: 251014Hom.: 184 AF XY: 0.0366 AC XY: 4962AN XY: 135622
GnomAD4 exome AF: 0.0423 AC: 61765AN: 1459644Hom.: 1431 Cov.: 53 AF XY: 0.0421 AC XY: 30559AN XY: 726252
GnomAD4 genome AF: 0.0312 AC: 4710AN: 150756Hom.: 116 Cov.: 30 AF XY: 0.0307 AC XY: 2255AN XY: 73570
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at