chrX-152990660-C-A

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.51
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PNMA5NM_001184924.2 linkc.939G>T p.Gly313Gly synonymous_variant Exon 4 of 4 ENST00000535214.6 NP_001171853.1 Q96PV4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PNMA5ENST00000535214.6 linkc.939G>T p.Gly313Gly synonymous_variant Exon 4 of 4 3 NM_001184924.2 ENSP00000445775.1 Q96PV4
PNMA5ENST00000361887.5 linkc.939G>T p.Gly313Gly synonymous_variant Exon 2 of 2 1 ENSP00000354834.5 Q96PV4
PNMA5ENST00000439251.3 linkc.939G>T p.Gly313Gly synonymous_variant Exon 2 of 2 1 ENSP00000388850.1 Q96PV4
PNMA5ENST00000452693.5 linkc.939G>T p.Gly313Gly synonymous_variant Exon 3 of 3 2 ENSP00000392342.1 Q96PV4

Frequencies

GnomAD3 genomes
AF:
0.000249
AC:
28
AN:
112386
Hom.:
0
Cov.:
24
AF XY:
0.000289
AC XY:
10
AN XY:
34560
show subpopulations
Gnomad AFR
AF:
0.000421
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00511
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000792
AC:
118
AN:
149029
Hom.:
0
AF XY:
0.00122
AC XY:
58
AN XY:
47533
show subpopulations
Gnomad AFR exome
AF:
0.000159
Gnomad AMR exome
AF:
0.0000963
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00960
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000144
Gnomad OTH exome
AF:
0.000567
GnomAD4 exome
AF:
0.000405
AC:
431
AN:
1065351
Hom.:
4
Cov.:
31
AF XY:
0.000686
AC XY:
237
AN XY:
345313
show subpopulations
Gnomad4 AFR exome
AF:
0.000202
Gnomad4 AMR exome
AF:
0.0000709
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00836
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000362
Gnomad4 OTH exome
AF:
0.000426
GnomAD4 genome
AF:
0.000249
AC:
28
AN:
112439
Hom.:
0
Cov.:
24
AF XY:
0.000289
AC XY:
10
AN XY:
34623
show subpopulations
Gnomad4 AFR
AF:
0.000420
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00513
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000188
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000131
Hom.:
1
Bravo
AF:
0.000102

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

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
2.5
DANN
Benign
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs144825466; hg19: chrX-152159204; API