Variant chrX-125321662-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001195272.2(TEX13C):c.1543C>A(p.Leu515Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L515L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00077 ( 1 hom., 0 hem., cov: 20)

Exomes 𝑓: 0.0011 ( 3 hom. 226 hem. )

Failed GnomAD Quality Control

Consequence

TEX13C
NM_001195272.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0440

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.01839301).

BP6

Variant X-125321662-C-A is Benign according to our data. Variant chrX-125321662-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661375.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2 linkuse as main transcript	c.1543C>A	p.Leu515Met	missense_variant	1/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
TEX13C	ENST00000695840.1 linkuse as main transcript	c.1543C>A	p.Leu515Met	missense_variant	1/2	NM_001195272.2	P1
TEX13C	ENST00000632600.2 linkuse as main transcript	c.1543C>A	p.Leu515Met	missense_variant	1/1		P1
TEX13C	ENST00000695841.1 linkuse as main transcript	c.1543C>A	p.Leu515Met	missense_variant	1/2		P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

82080

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

21294

FAILED QC

Gnomad AFR

AF:

0.000137

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00339

Gnomad MID

AF:

0.0119

Gnomad NFE

AF:

0.00105

Gnomad OTH

AF:

0.000921

GnomAD3 exomes

AF:

0.000184

AC:

AN:

87088

Hom.:

AF XY:

0.000403

AC XY:

AN XY:

32282

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000614

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000504

Gnomad NFE exome

AF:

0.000285

Gnomad OTH exome

AF:

0.00112

GnomAD4 exome

AF:

0.00113

AC:

432

AN:

380719

Hom.:

Cov.:

AF XY:

0.00162

AC XY:

226

AN XY:

139397

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000349

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00651

Gnomad4 NFE exome

AF:

0.00112

Gnomad4 OTH exome

AF:

0.000831

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000767

AC:

AN:

82121

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

21323

show subpopulations

Gnomad4 AFR

AF:

0.000137

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00339

Gnomad4 NFE

AF:

0.00105

Gnomad4 OTH

AF:

0.000911

Alfa

AF:

0.00148

Hom.:

ExAC

AF:

0.000127

AC:

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

Jan 01, 2024

TEX13C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.049

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.32

DANN

Benign

0.21

DEOGEN2

Benign

0.0025

FATHMM_MKL

Benign

0.000070

LIST_S2

Benign

0.14

MetaRNN

Benign

0.018

PrimateAI

Benign

0.25

Sift4G

Benign

0.29

Vest4

0.040

GERP RS

0.22

Varity_R

0.083

gMVP

0.021

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