Genetic Variant PNMA6E:p.Ala271Ala (chrX-153398037-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001367770.1(PNMA6E):c.813A>G(p.Ala271Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 446,183 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00010 ( 0 hom., 3 hem., cov: 23)

Exomes 𝑓: 0.00013 ( 0 hom. 15 hem. )

Consequence

PNMA6E
NM_001367770.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.619

Variant links:

Genes affected

PNMA6E (HGNC:50767): (PNMA family member 6E)

PNMA6E links:

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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=-0.87).

BP6

Variant X-153398037-T-C is Benign according to our data. Variant chrX-153398037-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2661681.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.619 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
PNMA6E	NM_001367770.1 link	c.813A>G	p.Ala271Ala	synonymous_variant	Exon 2 of 2	ENST00000445091.3	NP_001354699.1
PNMA6E	XM_047442374.1 link	c.813A>G	p.Ala271Ala	synonymous_variant	Exon 2 of 2		XP_047298330.1
PNMA6E	NM_001351293.2 link	c.144-165A>G		intron_variant	Intron 2 of 2		NP_001338222.1
PNMA6E	NM_001351294.2 link	c.144-165A>G		intron_variant	Intron 2 of 2		NP_001338223.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNMA6E	ENST00000445091.3 link	c.813A>G	p.Ala271Ala	synonymous_variant	Exon 2 of 2	2	NM_001367770.1	ENSP00000488500.1		A0A0J9YXQ4
PNMA6E	ENST00000633844.1 link	c.144-165A>G		intron_variant	Intron 2 of 2	3		ENSP00000488404.1		A0A0J9YXH5

Frequencies

GnomAD3 genomes

AF:

0.0000997

AC:

AN:

110338

Hom.:

Cov.:

AF XY:

0.0000917

AC XY:

AN XY:

32724

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000394

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000190

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000125

AC:

AN:

335797

Hom.:

Cov.:

AF XY:

0.000130

AC XY:

AN XY:

115295

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000871

Gnomad4 SAS exome

AF:

0.000259

Gnomad4 FIN exome

AF:

0.000176

Gnomad4 NFE exome

AF:

0.000142

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000997

AC:

AN:

110386

Hom.:

Cov.:

AF XY:

0.0000915

AC XY:

AN XY:

32782

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000394

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000190

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000432

Hom.:

Bravo

AF:

0.0000453

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PNMA6E: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.91

DANN

Benign

0.33

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over