dbSNP rs3830028: PNMA3:c.*1122T>C (chrX-153059569-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013364.6(PNMA3):c.*1122T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.93 ( 34065 hom., 30987 hem., cov: 23)

Exomes 𝑓: 0.98 ( 3747 hom. 3493 hem. )

Failed GnomAD Quality Control

Consequence

PNMA3
NM_013364.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.00

Publications

0 publications found

Variant links:

Genes affected

PNMA3 (HGNC:18742): (PNMA family member 3) The protein encoded by this gene belongs to the paraneoplastic antigen MA (PNMA) family, which shares homology with retroviral Gag proteins. The PNMA antigens are highly expressed in the brain and also in a range of tumors associated with serious neurological phenotypes. PMID:16407312 reports the presence of a functional -1 ribosomal frameshift signal (consisting of a heptanucleotide shift motif followed 3' by a pseudoknot structure) in this gene, however, the frame-shifted product has not been characterized. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

PNMA3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
PNMA3	NM_013364.6 link	c.*1122T>C	3_prime_UTR_variant	Exon 2 of 2	ENST00000593810.3	NP_037496.4
PNMA3	XR_938508.4 link	n.2277T>C	non_coding_transcript_exon_variant	Exon 3 of 3
PNMA3	NM_001282535.2 link	c.*1025T>C	3_prime_UTR_variant	Exon 3 of 3		NP_001269464.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
PNMA3	ENST00000593810.3 link	c.*1122T>C	3_prime_UTR_variant	Exon 2 of 2	6	NM_013364.6	ENSP00000469445.1
PNMA3	ENST00000619635.1 link	c.*1025T>C	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000480719.1
PNMA3	ENST00000424805.1 link	n.*610T>C	non_coding_transcript_exon_variant	Exon 3 of 3	5		ENSP00000390576.1
PNMA3	ENST00000424805.1 link	n.*610T>C	3_prime_UTR_variant	Exon 3 of 3	5		ENSP00000390576.1

Frequencies

GnomAD3 genomes

AF:

0.931

AC:

103475

AN:

111090

Hom.:

34070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.963

Gnomad AMI

AF:

0.949

Gnomad AMR

AF:

0.806

Gnomad ASJ

AF:

0.975

Gnomad EAS

AF:

0.563

Gnomad SAS

AF:

0.933

Gnomad FIN

AF:

0.976

Gnomad MID

AF:

0.932

Gnomad NFE

AF:

0.956

Gnomad OTH

AF:

0.904

GnomAD4 exome

AF:

0.977

AC:

11164

AN:

11431

Hom.:

3747

Cov.:

AF XY:

0.978

AC XY:

3493

AN XY:

3573

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.667

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.667

AC:

AN:

South Asian (SAS)

AF:

0.667

AC:

AN:

European-Finnish (FIN)

AF:

0.977

AC:

10934

AN:

11186

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.954

AC:

146

AN:

153

Other (OTH)

AF:

0.958

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.931

AC:

103516

AN:

111144

Hom.:

34065

Cov.:

AF XY:

0.930

AC XY:

30987

AN XY:

33336

show subpopulations

African (AFR)

AF:

0.963

AC:

29450

AN:

30597

American (AMR)

AF:

0.805

AC:

8586

AN:

10671

Ashkenazi Jewish (ASJ)

AF:

0.975

AC:

2576

AN:

2641

East Asian (EAS)

AF:

0.563

AC:

1922

AN:

3416

South Asian (SAS)

AF:

0.933

AC:

2400

AN:

2572

European-Finnish (FIN)

AF:

0.976

AC:

5843

AN:

5989

Middle Eastern (MID)

AF:

0.931

AC:

201

AN:

216

European-Non Finnish (NFE)

AF:

0.956

AC:

50527

AN:

52854

Other (OTH)

AF:

0.906

AC:

1372

AN:

1515

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

243

486

730

973

1216

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.946

Hom.:

8556

Bravo

AF:

0.912

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.15

(source)

PhyloP100

-4.0

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over