X-125320245-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001195272.2(TEX13C):c.126G>A(p.Pro42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000873 in 515,313 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 25 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000088 (0 hom., 3 hem., cov: 25)
  • Exomes 𝑓: 0.000087 (0 hom. 22 hem.)
• Consequence: TEX13C NM_001195272.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.752

Genes affected

TEX13C (HGNC:52277): (TEX13 family member C) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant X-125320245-G-A is Benign according to our data. Variant chrX-125320245-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661371.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.752 with no splicing effect.
• BS2: High Hemizygotes in GnomAd at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2	c.126G>A	p.Pro42=	synonymous_variant	1/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX13C	ENST00000695840.1	c.126G>A	p.Pro42=	synonymous_variant	1/2		NM_001195272.2	P1
TEX13C	ENST00000632600.2	c.126G>A	p.Pro42=	synonymous_variant	1/1			P1
TEX13C	ENST00000695841.1	c.126G>A	p.Pro42=	synonymous_variant	1/2			P1

Frequencies

GnomAD3 genomes AF: 0.0000878 AC: 10 AN: 113845 Hom.: 0 Cov.: 25 AF XY: 0.0000834 AC XY: 3 AN XY: 35965

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000915

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: 0.000168

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000820 AC: 8 AN: 97593 Hom.: 0 AF XY: 0.0000825 AC XY: 3 AN XY: 36353

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000104

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: 0.000157

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000872 AC: 35 AN: 401415 Hom.: 0 Cov.: 0 AF XY: 0.000148 AC XY: 22 AN XY: 148913

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000111

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000781

Gnomad4 NFE exome AF: 0.000120

Gnomad4 OTH exome AF: 0.0000865

GnomAD4 genome AF: 0.0000878 AC: 10 AN: 113898 Hom.: 0 Cov.: 25 AF XY: 0.0000833 AC XY: 3 AN XY: 36028

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000914

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000168

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

TEX13C: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs113566377; hg19: chrX-124454094; COSMIC: COSV65987122;