X-125320726-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001195272.2(TEX13C):c.607C>A(p.Pro203Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000261 in 513,932 control chromosomes in the GnomAD database, including 1 homozygotes. There are 38 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 0.00081 (0 hom., 25 hem., cov: 25)
  • Exomes 𝑓: 0.00011 (1 hom. 13 hem.)
• Consequence: TEX13C NM_001195272.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.314

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.007995307).
• BP6: Variant X-125320726-C-A is Benign according to our data. Variant chrX-125320726-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661372.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2	c.607C>A	p.Pro203Thr	missense_variant	1/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX13C	ENST00000695840.1	c.607C>A	p.Pro203Thr	missense_variant	1/2		NM_001195272.2	P1
TEX13C	ENST00000632600.2	c.607C>A	p.Pro203Thr	missense_variant	1/1			P1
TEX13C	ENST00000695841.1	c.607C>A	p.Pro203Thr	missense_variant	1/2			P1

Frequencies

GnomAD3 genomes AF: 0.000811 AC: 91 AN: 112228 Hom.: 0 Cov.: 25 AF XY: 0.000727 AC XY: 25 AN XY: 34408

Gnomad AFR AF: 0.00272

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000562

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: 0.00

Gnomad OTH AF: 0.000663

GnomAD3 exomes AF: 0.000143 AC: 14 AN: 97918 Hom.: 0 AF XY: 0.0000819 AC XY: 3 AN XY: 36614

Gnomad AFR exome AF: 0.00273

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: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000107 AC: 43 AN: 401653 Hom.: 1 Cov.: 0 AF XY: 0.0000872 AC XY: 13 AN XY: 149067

Gnomad4 AFR exome AF: 0.00272

Gnomad4 AMR exome AF: 0.000221

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: 0.00

Gnomad4 OTH exome AF: 0.000130

GnomAD4 genome AF: 0.000810 AC: 91 AN: 112279 Hom.: 0 Cov.: 25 AF XY: 0.000725 AC XY: 25 AN XY: 34469

Gnomad4 AFR AF: 0.00272

Gnomad4 AMR AF: 0.000561

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.000654

Alfa AF: 0.000591 Hom.: 5

Bravo AF: 0.000793

ExAC AF: 0.0000576 AC: 1

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

Dec 01, 2022

TEX13C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_noAF	Benign	-0.87
Cadd	Benign	12
Dann	Benign	0.66
DEOGEN2	Benign	0.029	T
FATHMM_MKL	Benign	0.027	N
LIST_S2	Benign	0.35	T
MetaRNN	Benign	0.0080	T
PrimateAI	Benign	0.23	T
Sift4G	Benign	0.083	T
Vest4		0.036
GERP RS		-2.3
Varity_R		0.046
gMVP		0.16

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

Other links and lift over

dbSNP: rs192356374; hg19: chrX-124454575;