13-30932754-C-T

Position:

• chr13-30932754-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_152325.3(TEX26):​c.39C>T​(p.Leu13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00087 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0012 (0 hom.)
• Consequence: TEX26 NM_152325.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.104

Genes affected

TEX26 (HGNC:28622): (testis expressed 26) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TEX26-AS1 (HGNC:42784): (TEX26 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 13-30932754-C-T is Benign according to our data. Variant chr13-30932754-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643713.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.104 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX26	NM_152325.3	c.39C>T	p.Leu13=	synonymous_variant	1/7	ENST00000380473.8	NP_689538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX26	ENST00000380473.8	c.39C>T	p.Leu13=	synonymous_variant	1/7	1	NM_152325.3	ENSP00000369840	P1

Frequencies

GnomAD3 genomes AF: 0.000874 AC: 133 AN: 152238 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00164

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000376

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00132

Gnomad OTH AF: 0.000955

GnomAD3 exomes AF: 0.000850 AC: 212 AN: 249546 Hom.: 0 AF XY: 0.000880 AC XY: 119 AN XY: 135262

Gnomad AFR exome AF: 0.000252

Gnomad AMR exome AF: 0.00110

Gnomad ASJ exome AF: 0.000398

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000371

Gnomad NFE exome AF: 0.00131

Gnomad OTH exome AF: 0.00164

GnomAD4 exome AF: 0.00122 AC: 1780 AN: 1461602 Hom.: 0 Cov.: 30 AF XY: 0.00116 AC XY: 840 AN XY: 727098

Gnomad4 AFR exome AF: 0.000179

Gnomad4 AMR exome AF: 0.00143

Gnomad4 ASJ exome AF: 0.000689

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000432

Gnomad4 NFE exome AF: 0.00142

Gnomad4 OTH exome AF: 0.00142

GnomAD4 genome AF: 0.000873 AC: 133 AN: 152356 Hom.: 0 Cov.: 32 AF XY: 0.000859 AC XY: 64 AN XY: 74508

Gnomad4 AFR AF: 0.000216

Gnomad4 AMR AF: 0.00163

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000376

Gnomad4 NFE AF: 0.00132

Gnomad4 OTH AF: 0.000945

Alfa AF: 0.00111 Hom.: 0

Bravo AF: 0.00108

EpiCase AF: 0.000981

EpiControl AF: 0.00172

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

TEX26: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.60
DANN	Benign	0.61

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: rs140143587; hg19: chr13-31506891;