Variant X-125321671-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.1552C>A(p.Leu518Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000324 in 101,752 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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. L518L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00032 ( 0 hom., 0 hem., cov: 21)

Exomes 𝑓: 0.00058 ( 3 hom. 184 hem. )

Failed GnomAD Quality Control

Consequence

TEX13C
NM_001195272.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.423

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=0.062064648).

BP6

Variant X-125321671-C-A is Benign according to our data. Variant chrX-125321671-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661377.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAdExome at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2 linkuse as main transcript	c.1552C>A	p.Leu518Met	missense_variant	1/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
TEX13C	ENST00000695840.1 linkuse as main transcript	c.1552C>A	p.Leu518Met	missense_variant	1/2	NM_001195272.2	P1
TEX13C	ENST00000632600.2 linkuse as main transcript	c.1552C>A	p.Leu518Met	missense_variant	1/1		P1
TEX13C	ENST00000695841.1 linkuse as main transcript	c.1552C>A	p.Leu518Met	missense_variant	1/2		P1

Frequencies

GnomAD3 genomes

AF:

0.000324

AC:

AN:

101705

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

30467

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:

0.000870

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000539

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000123

AC:

AN:

97656

Hom.:

AF XY:

0.000302

AC XY:

AN XY:

36484

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000520

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000713

Gnomad FIN exome

AF:

0.000497

Gnomad NFE exome

AF:

0.000131

Gnomad OTH exome

AF:

0.000979

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000584

AC:

231

AN:

395397

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

184

AN XY:

147813

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000188

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000264

Gnomad4 FIN exome

AF:

0.00349

Gnomad4 NFE exome

AF:

0.000561

Gnomad4 OTH exome

AF:

0.000357

GnomAD4 genome

AF:

0.000324

AC:

AN:

101752

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

30518

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:

0.000870

Gnomad4 NFE

AF:

0.000539

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00154

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

Jul 01, 2023

TEX13C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_noAF

Benign

-0.94

Cadd

Benign

Dann

Benign

0.37

DEOGEN2

Benign

0.040

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.22

MetaRNN

Benign

0.062

PrimateAI

Benign

0.20

Sift4G

Benign

0.14

Vest4

0.12

GERP RS

-1.3

Varity_R

0.068

gMVP

0.024

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