rs12857479

Positions:

• chr13-30956872-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_152325.3(TEX26):​c.313-1G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,611,554 control chromosomes in the GnomAD database, including 107,389 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.29 (7485 hom., cov: 31)
  • Exomes 𝑓: 0.37 (99904 hom.)
• Consequence: TEX26 NM_152325.3 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

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

TEX26 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX26	NM_152325.3	c.313-1G>A		splice_acceptor_variant, intron_variant		ENST00000380473.8	NP_689538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX26	ENST00000380473.8	c.313-1G>A		splice_acceptor_variant, intron_variant		1	NM_152325.3	ENSP00000369840.3
TEX26	ENST00000531960.1	n.138-1G>A		splice_acceptor_variant, intron_variant		3		ENSP00000435263.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43700 AN: 151896 Hom.: 7486 Cov.: 31

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.330

GnomAD3 exomes AF: 0.345 AC: 86593 AN: 250808 Hom.: 15696 AF XY: 0.353 AC XY: 47878 AN XY: 135574

Gnomad AFR exome AF: 0.0850

Gnomad AMR exome AF: 0.312

Gnomad ASJ exome AF: 0.401

Gnomad EAS exome AF: 0.303

Gnomad SAS exome AF: 0.370

Gnomad FIN exome AF: 0.402

Gnomad NFE exome AF: 0.376

Gnomad OTH exome AF: 0.373

GnomAD4 exome AF: 0.366 AC: 533819 AN: 1459542 Hom.: 99904 Cov.: 33 AF XY: 0.368 AC XY: 267235 AN XY: 726220

Gnomad4 AFR exome AF: 0.0871

Gnomad4 AMR exome AF: 0.312

Gnomad4 ASJ exome AF: 0.407

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.370

Gnomad4 FIN exome AF: 0.397

Gnomad4 NFE exome AF: 0.377

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.287 AC: 43703 AN: 152012 Hom.: 7485 Cov.: 31 AF XY: 0.290 AC XY: 21536 AN XY: 74268

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.330

Alfa AF: 0.355 Hom.: 21042

Bravo AF: 0.273

TwinsUK AF: 0.380 AC: 1408

ALSPAC AF: 0.383 AC: 1478

ESP6500AA AF: 0.0994 AC: 438

ESP6500EA AF: 0.370 AC: 3185

ExAC AF: 0.342 AC: 41499

Asia WGS AF: 0.306 AC: 1065 AN: 3478

EpiCase AF: 0.368

EpiControl AF: 0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.58	T
BayesDel_noAF	Benign	-0.46
CADD	Uncertain	24
DANN	Benign	0.92
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Benign	0.72	D
GERP RS		4.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.79
SpliceAI score (max)		0.54		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.54		Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12857479; hg19: chr13-31531009; COSMIC: COSV66839414; COSMIC: COSV66839414;