Variant X-125322683-G-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.2564G>A(p.Ser855Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000488 in 512,527 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 83 hemizygotes 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 (★).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., 6 hem., cov: 23)

Exomes 𝑓: 0.00053 ( 0 hom. 77 hem. )

Consequence

TEX13C
NM_001195272.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0590

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=0.051112443).

BP6

Variant X-125322683-G-A is Benign according to our data. Variant chrX-125322683-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661379.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-125322683-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2 linkuse as main transcript	c.2564G>A	p.Ser855Asn	missense_variant	1/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
TEX13C	ENST00000695840.1 linkuse as main transcript	c.2564G>A	p.Ser855Asn	missense_variant	1/2	NM_001195272.2	P1
TEX13C	ENST00000632600.2 linkuse as main transcript	c.2564G>A	p.Ser855Asn	missense_variant	1/1		P1
TEX13C	ENST00000695841.1 linkuse as main transcript	c.2564G>A	p.Ser855Asn	missense_variant	1/2		P1

Frequencies

GnomAD3 genomes

AF:

0.000334

AC:

AN:

110919

Hom.:

Cov.:

AF XY:

0.000181

AC XY:

AN XY:

33203

show subpopulations

Gnomad AFR

AF:

0.000131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000948

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:

0.000605

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000409

AC:

AN:

97904

Hom.:

AF XY:

0.000382

AC XY:

AN XY:

36608

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

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:

0.000989

Gnomad OTH exome

AF:

0.000651

GnomAD4 exome

AF:

0.000530

AC:

213

AN:

401608

Hom.:

Cov.:

AF XY:

0.000517

AC XY:

AN XY:

149052

show subpopulations

Gnomad4 AFR exome

AF:

0.0000800

Gnomad4 AMR exome

AF:

0.00

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:

0.000890

Gnomad4 OTH exome

AF:

0.000173

GnomAD4 genome

AF:

0.000334

AC:

AN:

110919

Hom.:

Cov.:

AF XY:

0.000181

AC XY:

AN XY:

33203

show subpopulations

Gnomad4 AFR

AF:

0.000131

Gnomad4 AMR

AF:

0.0000948

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000605

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000641

Hom.:

Bravo

AF:

0.000393

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00

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, 2023

TEX13C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_noAF

Benign

-0.85

Cadd

Benign

Dann

Benign

0.48

DEOGEN2

Benign

0.015

FATHMM_MKL

Benign

0.022

LIST_S2

Benign

0.33

MetaRNN

Benign

0.051

PrimateAI

Benign

0.29

Sift4G

Pathogenic

0.0

Vest4

0.058

GERP RS

-0.97

Varity_R

0.086

gMVP

0.065

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