rs2230680
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002816.5(PSMD12):āc.1073T>Cā(p.Val358Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000419 in 1,608,002 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002816.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMD12 | NM_002816.5 | c.1073T>C | p.Val358Ala | missense_variant | 9/11 | ENST00000356126.8 | |
PSMD12 | NM_174871.4 | c.1013T>C | p.Val338Ala | missense_variant | 8/10 | ||
PSMD12 | NM_001316341.2 | c.896T>C | p.Val299Ala | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMD12 | ENST00000356126.8 | c.1073T>C | p.Val358Ala | missense_variant | 9/11 | 1 | NM_002816.5 | P1 | |
PSMD12 | ENST00000584008.5 | c.*1228T>C | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 | 1 | ||||
PSMD12 | ENST00000357146.4 | c.1013T>C | p.Val338Ala | missense_variant | 8/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00220 AC: 335AN: 152182Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000605 AC: 151AN: 249582Hom.: 3 AF XY: 0.000489 AC XY: 66AN XY: 135026
GnomAD4 exome AF: 0.000232 AC: 338AN: 1455702Hom.: 4 Cov.: 31 AF XY: 0.000211 AC XY: 153AN XY: 723880
GnomAD4 genome ? AF: 0.00221 AC: 336AN: 152300Hom.: 2 Cov.: 33 AF XY: 0.00218 AC XY: 162AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | PSMD12: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at