Variant X-125321673-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.1554G>A(p.Leu518=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000296 in 101,492 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. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00030 ( 0 hom., 0 hem., cov: 21)

Exomes 𝑓: 0.00056 ( 3 hom. 176 hem. )

Failed GnomAD Quality Control

Consequence

TEX13C
NM_001195272.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.565

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=-0.94).

BP6

Variant X-125321673-G-A is Benign according to our data. Variant chrX-125321673-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661378.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.565 with no splicing effect.

BS2

High Hemizygotes in GnomAdExome at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2 linkuse as main transcript	c.1554G>A	p.Leu518=	synonymous_variant	1/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
TEX13C	ENST00000695840.1 linkuse as main transcript	c.1554G>A	p.Leu518=	synonymous_variant	1/2	NM_001195272.2	P1
TEX13C	ENST00000632600.2 linkuse as main transcript	c.1554G>A	p.Leu518=	synonymous_variant	1/1		P1
TEX13C	ENST00000695841.1 linkuse as main transcript	c.1554G>A	p.Leu518=	synonymous_variant	1/2		P1

Frequencies

GnomAD3 genomes

AF:

0.000296

AC:

AN:

101444

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

30294

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:

0.000874

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000482

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000102

AC:

AN:

97661

Hom.:

AF XY:

0.000274

AC XY:

AN XY:

36481

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:

0.00

Gnomad FIN exome

AF:

0.000497

Gnomad NFE exome

AF:

0.000104

Gnomad OTH exome

AF:

0.000980

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000556

AC:

220

AN:

395409

Hom.:

Cov.:

AF XY:

0.00119

AC XY:

176

AN XY:

147795

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:

0.00

Gnomad4 FIN exome

AF:

0.00329

Gnomad4 NFE exome

AF:

0.000548

Gnomad4 OTH exome

AF:

0.000268

GnomAD4 genome

AF:

0.000296

AC:

AN:

101492

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

30342

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:

0.000874

Gnomad4 NFE

AF:

0.000482

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00135

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

Jan 01, 2024

TEX13C: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

Cadd

Benign

1.7

Dann

Benign

0.19

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