Variant X-125321472-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001195272.2(TEX13C):c.1353G>A(p.Glu451Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000602 in 508,018 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 104 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 0.00053 ( 0 hom., 11 hem., cov: 23)

Exomes 𝑓: 0.00062 ( 0 hom. 93 hem. )

Consequence

TEX13C
NM_001195272.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.258

Variant links:

Genes affected

TEX13C (HGNC:52277): (TEX13 family member C) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

TEX13C links:

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=-0.9).

BP6

Variant X-125321472-G-A is Benign according to our data. Variant chrX-125321472-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661373.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.258 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX13C	NM_001195272.2 linkuse as main transcript	c.1353G>A	p.Glu451Glu	synonymous_variant	1/2	ENST00000695840.1	NP_001182201.1	A0A0J9YWL9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TEX13C	ENST00000695840.1 linkuse as main transcript	c.1353G>A	p.Glu451Glu	synonymous_variant	1/2		NM_001195272.2	ENSP00000512212.1	A0A0J9YWL9
TEX13C	ENST00000632600.2 linkuse as main transcript	c.1353G>A	p.Glu451Glu	synonymous_variant	1/1	6		ENSP00000488022.1	A0A0J9YWL9
TEX13C	ENST00000695841.1 linkuse as main transcript	c.1353G>A	p.Glu451Glu	synonymous_variant	1/2			ENSP00000512213.1	A0A0J9YWL9

Frequencies

GnomAD3 genomes

AF:

0.000530

AC:

AN:

107491

Hom.:

Cov.:

AF XY:

0.000353

AC XY:

AN XY:

31175

show subpopulations

Gnomad AFR

AF:

0.0000684

Gnomad AMI

AF:

0.00154

Gnomad AMR

AF:

0.000484

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:

0.000889

Gnomad OTH

AF:

0.00210

GnomAD3 exomes

AF:

0.000531

AC:

AN:

97876

Hom.:

AF XY:

0.000464

AC XY:

AN XY:

36612

show subpopulations

Gnomad AFR exome

AF:

0.000195

Gnomad AMR exome

AF:

0.000779

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000807

Gnomad OTH exome

AF:

0.00163

GnomAD4 exome

AF:

0.000622

AC:

249

AN:

400462

Hom.:

Cov.:

AF XY:

0.000627

AC XY:

AN XY:

148414

show subpopulations

Gnomad4 AFR exome

AF:

0.000241

Gnomad4 AMR exome

AF:

0.000888

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000889

Gnomad4 OTH exome

AF:

0.000651

GnomAD4 genome

AF:

0.000530

AC:

AN:

107556

Hom.:

Cov.:

AF XY:

0.000352

AC XY:

AN XY:

31232

show subpopulations

Gnomad4 AFR

AF:

0.0000683

Gnomad4 AMR

AF:

0.000484

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000889

Gnomad4 OTH

AF:

0.00207

Alfa

AF:

0.000240

Hom.:

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

Apr 01, 2022

TEX13C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.52

DANN

Benign

0.29

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