dbSNP rs782467318: PNMA5:p.Gly428Val (chrX-152990316-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001184924.2(PNMA5):c.1283G>T(p.Gly428Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G428A) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 24)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

PNMA5
NM_001184924.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.65

Publications

0 publications found

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]

PNMA5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.044469535).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001184924.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PNMA5	NM_001184924.2	MANE Select	c.1283G>T	p.Gly428Val	missense	Exon 4 of 4	NP_001171853.1	Q96PV4
PNMA5	NM_001103150.1		c.1283G>T	p.Gly428Val	missense	Exon 2 of 2	NP_001096620.1	Q96PV4
PNMA5	NM_001103151.1		c.1283G>T	p.Gly428Val	missense	Exon 3 of 3	NP_001096621.1	Q96PV4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PNMA5	ENST00000535214.6	TSL:3 MANE Select	c.1283G>T	p.Gly428Val	missense	Exon 4 of 4	ENSP00000445775.1	Q96PV4
PNMA5	ENST00000361887.5	TSL:1	c.1283G>T	p.Gly428Val	missense	Exon 2 of 2	ENSP00000354834.5	Q96PV4
PNMA5	ENST00000439251.3	TSL:1	c.1283G>T	p.Gly428Val	missense	Exon 2 of 2	ENSP00000388850.1	Q96PV4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

125038

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1036493

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

334285

African (AFR)

AF:

0.00

AC:

AN:

23803

American (AMR)

AF:

0.00

AC:

AN:

22143

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14983

East Asian (EAS)

AF:

0.00

AC:

AN:

29137

South Asian (SAS)

AF:

0.00

AC:

AN:

43190

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38163

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3828

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

817940

Other (OTH)

AF:

0.00

AC:

AN:

43306

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.011

(source)

DANN

Benign

0.49

DEOGEN2

Benign

0.010

FATHMM_MKL

Benign

0.0011

LIST_S2

Benign

0.24

M_CAP

Benign

0.0019

MetaRNN

Benign

0.044

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.34

PhyloP100

-3.7

PrimateAI

Benign

0.26

PROVEAN

Benign

0.59

REVEL

Benign

0.010

Sift

Benign

0.31

Sift4G

Benign

0.98

Polyphen

0.0

Vest4

0.057

MutPred

0.21

Gain of helix (P = 0.0128)

MVP

0.076

MPC

0.12

ClinPred

0.31

GERP RS

-5.5

Varity_R

0.043

gMVP

0.21

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over