1-13773182-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001393986.1(PRDM2):c.616G>A(p.Ala206Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000485 in 1,544,930 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A206S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001393986.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRDM2 | NM_001393986.1 | c.616G>A | p.Ala206Thr | missense_variant | 7/10 | ENST00000311066.10 | NP_001380915.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000315 AC: 6AN: 190752Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 102588
GnomAD4 exome AF: 0.0000309 AC: 43AN: 1392582Hom.: 0 Cov.: 28 AF XY: 0.0000304 AC XY: 21AN XY: 690710
GnomAD4 genome AF: 0.000210 AC: 32AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2024 | The c.616G>A (p.A206T) alteration is located in exon 7 (coding exon 6) of the PRDM2 gene. This alteration results from a G to A substitution at nucleotide position 616, causing the alanine (A) at amino acid position 206 to be replaced by a threonine (T). 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