chrX-152990660-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001184924.2(PNMA5):c.939G>T(p.Gly313Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00039 in 1,177,790 control chromosomes in the GnomAD database, including 4 homozygotes. There are 247 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00025 ( 0 hom., 10 hem., cov: 24)
Exomes 𝑓: 0.00040 ( 4 hom. 237 hem. )
Consequence
PNMA5
NM_001184924.2 synonymous
NM_001184924.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.51
Genes affected
PNMA5 (HGNC:18743): (PNMA family member 5) This gene encodes a member of the paraneoplastic Ma antigen protein family. These proteins have been implicated in the development of paraneoplastic disorders resulting from an immune response directed against them. Paraneoplastic disorders are the result of an abnormal immune response to a tumor. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant X-152990660-C-A is Benign according to our data. Variant chrX-152990660-C-A is described in ClinVar as [Benign]. Clinvar id is 756325.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.51 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 10 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNMA5 | ENST00000535214.6 | c.939G>T | p.Gly313Gly | synonymous_variant | Exon 4 of 4 | 3 | NM_001184924.2 | ENSP00000445775.1 | ||
PNMA5 | ENST00000361887.5 | c.939G>T | p.Gly313Gly | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000354834.5 | |||
PNMA5 | ENST00000439251.3 | c.939G>T | p.Gly313Gly | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000388850.1 | |||
PNMA5 | ENST00000452693.5 | c.939G>T | p.Gly313Gly | synonymous_variant | Exon 3 of 3 | 2 | ENSP00000392342.1 |
Frequencies
GnomAD3 genomes AF: 0.000249 AC: 28AN: 112386Hom.: 0 Cov.: 24 AF XY: 0.000289 AC XY: 10AN XY: 34560
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GnomAD3 exomes AF: 0.000792 AC: 118AN: 149029Hom.: 0 AF XY: 0.00122 AC XY: 58AN XY: 47533
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GnomAD4 exome AF: 0.000405 AC: 431AN: 1065351Hom.: 4 Cov.: 31 AF XY: 0.000686 AC XY: 237AN XY: 345313
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GnomAD4 genome AF: 0.000249 AC: 28AN: 112439Hom.: 0 Cov.: 24 AF XY: 0.000289 AC XY: 10AN XY: 34623
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 05, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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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