chr9-130664785-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021619.3(PRDM12):c.132G>A(p.Val44=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
PRDM12
NM_021619.3 synonymous
NM_021619.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.999
Genes affected
PRDM12 (HGNC:13997): (PR/SET domain 12) This gene encodes a transcriptional regulator of sensory neuronal specification that plays a critical role in pain perception. The encoded protein contains an N-terminal PRDI-BF1 and RIZ homology (PR) domain, a SET domain, and three C-terminal C2H2 zinc finger DNA-binding domains. Naturally occurring mutations in this gene are associated with congenital insensitivity to pain (CIP), and hereditary sensory and autonomic neuropathies (HSAN's) affecting peripheral sensory and autonomic neurons. Deregulation of this gene is associated with solid cancers and hematological malignancies including chronic myeloid leukaemia. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 9-130664785-G-A is Benign according to our data. Variant chr9-130664785-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1940218.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM12 | NM_021619.3 | c.132G>A | p.Val44= | synonymous_variant | 1/5 | ENST00000253008.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM12 | ENST00000253008.3 | c.132G>A | p.Val44= | synonymous_variant | 1/5 | 1 | NM_021619.3 | P1 | |
PRDM12 | ENST00000676323.1 | c.132G>A | p.Val44= | synonymous_variant | 1/6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448802Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 719816
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34
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
Asia WGS
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3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital insensitivity to pain-hypohidrosis syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 22, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at