Variant X-125321645-T-C 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.1526T>C(p.Leu509Pro) 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 (★).

Frequency

Genomes: 𝑓 0.0026 ( 2 hom., 3 hem., cov: 18)

Exomes 𝑓: 0.0018 ( 3 hom. 258 hem. )

Failed GnomAD Quality Control

Consequence

TEX13C
NM_001195272.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.28

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=0.010473281).

BP6

Variant X-125321645-T-C is Benign according to our data. Variant chrX-125321645-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2661374.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX13C	NM_001195272.2 linkuse as main transcript	c.1526T>C	p.Leu509Pro	missense_variant	1/2	ENST00000695840.1	NP_001182201.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	Appris
TEX13C	ENST00000695840.1 linkuse as main transcript	c.1526T>C	p.Leu509Pro	missense_variant	1/2	NM_001195272.2	ENSP00000512212	P1
TEX13C	ENST00000632600.2 linkuse as main transcript	c.1526T>C	p.Leu509Pro	missense_variant	1/1		ENSP00000488022	P1
TEX13C	ENST00000695841.1 linkuse as main transcript	c.1526T>C	p.Leu509Pro	missense_variant	1/2		ENSP00000512213	P1

Frequencies

GnomAD3 genomes

AF:

0.00262

AC:

180

AN:

68716

Hom.:

Cov.:

AF XY:

0.000165

AC XY:

AN XY:

18194

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00271

Gnomad AMR

AF:

0.000908

Gnomad ASJ

AF:

0.00172

Gnomad EAS

AF:

0.00108

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00901

Gnomad MID

AF:

0.0448

Gnomad NFE

AF:

0.00322

Gnomad OTH

AF:

0.00322

GnomAD3 exomes

AF:

0.000561

AC:

AN:

89078

Hom.:

AF XY:

0.000515

AC XY:

AN XY:

33000

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000289

Gnomad ASJ exome

AF:

0.000171

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00205

Gnomad NFE exome

AF:

0.000904

Gnomad OTH exome

AF:

0.00144

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00178

AC:

631

AN:

354715

Hom.:

Cov.:

AF XY:

0.00196

AC XY:

258

AN XY:

131379

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000479

Gnomad4 ASJ exome

AF:

0.000160

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00952

Gnomad4 NFE exome

AF:

0.00182

Gnomad4 OTH exome

AF:

0.00134

GnomAD4 genome

AF:

0.00262

AC:

180

AN:

68772

Hom.:

Cov.:

AF XY:

0.000164

AC XY:

AN XY:

18240

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.000907

Gnomad4 ASJ

AF:

0.00172

Gnomad4 EAS

AF:

0.00108

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00901

Gnomad4 NFE

AF:

0.00322

Gnomad4 OTH

AF:

0.00318

Alfa

AF:

0.00689

Hom.:

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00381

AC:

ExAC

AF:

0.000249

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

Jun 01, 2024

TEX13C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.37

DANN

Benign

0.34

DEOGEN2

Benign

0.013

FATHMM_MKL

Benign

0.000040

LIST_S2

Benign

0.19

MetaRNN

Benign

0.010

PrimateAI

Benign

0.19

Sift4G

Benign

0.27

Vest4

0.042

GERP RS

-0.73

Varity_R

0.083

gMVP

0.012

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