Variant X-153398363-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_001367770.1(PNMA6E):c.487G>A(p.Ala163Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000019 ( 0 hom., 0 hem., cov: 19)

Exomes 𝑓: 0.000050 ( 0 hom. 4 hem. )

Consequence

PNMA6E
NM_001367770.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.550

Variant links:

Genes affected

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

PNMA6E links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.08732623).

BP6

Variant X-153398363-C-T is Benign according to our data. Variant chrX-153398363-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388852.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
PNMA6E	NM_001367770.1 linkuse as main transcript	c.487G>A	p.Ala163Thr	missense_variant	2/2	ENST00000445091.3	NP_001354699.1
PNMA6E	XM_047442374.1 linkuse as main transcript	c.487G>A	p.Ala163Thr	missense_variant	2/2		XP_047298330.1
PNMA6E	NM_001351293.2 linkuse as main transcript	c.143+344G>A		intron_variant			NP_001338222.1
PNMA6E	NM_001351294.2 linkuse as main transcript	c.143+344G>A		intron_variant			NP_001338223.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PNMA6E	ENST00000445091.3 linkuse as main transcript	c.487G>A	p.Ala163Thr	missense_variant	2/2	2	NM_001367770.1	ENSP00000488500.1		A0A0J9YXQ4
PNMA6E	ENST00000633844.1 linkuse as main transcript	c.143+344G>A		intron_variant		3		ENSP00000488404.1		A0A0J9YXH5

Frequencies

GnomAD3 genomes

AF:

0.0000194

AC:

AN:

103063

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

26585

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:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000397

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000495

AC:

AN:

302801

Hom.:

Cov.:

AF XY:

0.0000399

AC XY:

AN XY:

100215

show subpopulations

Gnomad4 AFR exome

AF:

0.000114

Gnomad4 AMR exome

AF:

0.0000825

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000944

Gnomad4 SAS exome

AF:

0.0000454

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000530

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000194

AC:

AN:

103063

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

26585

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:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000397

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2024

PNMA6E: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.48

DANN

Benign

0.72

DEOGEN2

Benign

0.0051

FATHMM_MKL

Benign

0.055

LIST_S2

Pathogenic

0.98

MetaRNN

Benign

0.087

Sift4G

Benign

0.087

Vest4

0.12

GERP RS

-3.4

Varity_R

0.026

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