13-30932754-C-T

Variant names:

• chr13-30932754-C-T
• rs140143587
• NM_152325.3:c.39C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001353388.2(TEX26):​c.-548C>T variant causes a 5 prime UTR premature start codon gain 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_001353388.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.104
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -6 ACMG points.

• 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 VariationId is 2643713.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353388.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX26	NM_152325.3	MANE Select	c.39C>T	p.Leu13Leu	synonymous	Exon 1 of 7	NP_689538.1	Q8N6G2
	TEX26	NM_001353388.2		c.-548C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 6	NP_001340317.1
	TEX26	NM_001353389.2		c.-270C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 6	NP_001340318.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX26	ENST00000380473.8	TSL:1 MANE Select	c.39C>T	p.Leu13Leu	synonymous	Exon 1 of 7	ENSP00000369840.3	Q8N6G2
	TEX26	ENST00000944411.1		c.39C>T	p.Leu13Leu	synonymous	Exon 1 of 4	ENSP00000614470.1
	TEX26	ENST00000944412.1		c.39C>T	p.Leu13Leu	synonymous	Exon 1 of 3	ENSP00000614471.1

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

GnomAD2 exomes AF: 0.000850 AC: 212 AN: 249546 AF XY: 0.000880

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 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

African (AFR) AF: 0.000179 AC: 6 AN: 33476

American (AMR) AF: 0.00143 AC: 64 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.000689 AC: 18 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86214

European-Finnish (FIN) AF: 0.000432 AC: 23 AN: 53256

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5768

European-Non Finnish (NFE) AF: 0.00142 AC: 1581 AN: 1111974

Other (OTH) AF: 0.00142 AC: 86 AN: 60358

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

African (AFR) AF: 0.000216 AC: 9 AN: 41590

American (AMR) AF: 0.00163 AC: 25 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.000376 AC: 4 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00132 AC: 90 AN: 68030

Other (OTH) AF: 0.000945 AC: 2 AN: 2116

Alfa AF: 0.00111 Hom.: 0

Bravo AF: 0.00108

EpiCase AF: 0.000981

EpiControl AF: 0.00172

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.60
DANN	Benign	0.61
PhyloP100		0.10
PromoterAI		-0.059	Neutral
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs140143587; hg19: chr13-31506891;