11-129910599-A-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_199437.2(PRDM10):c.3040T>A(p.Ser1014Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,613,640 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_199437.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM10 | NM_199437.2 | c.3040T>A | p.Ser1014Thr | missense_variant | 19/21 | ENST00000360871.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM10 | ENST00000360871.8 | c.3040T>A | p.Ser1014Thr | missense_variant | 19/21 | 1 | NM_199437.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00678 AC: 1032AN: 152122Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.00177 AC: 444AN: 250262Hom.: 4 AF XY: 0.00120 AC XY: 163AN XY: 135302
GnomAD4 exome AF: 0.000653 AC: 955AN: 1461400Hom.: 8 Cov.: 31 AF XY: 0.000539 AC XY: 392AN XY: 726972
GnomAD4 genome AF: 0.00679 AC: 1034AN: 152240Hom.: 12 Cov.: 33 AF XY: 0.00629 AC XY: 468AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at