dbSNP rs12857479: TEX26:c.313-1G>A (chr13-30956872-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

33 publications found

Variant links:

Genes affected

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

TEX26 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEX26	NM_152325.3 link	c.313-1G>A		splice_acceptor_variant, intron_variant	Intron 3 of 6	ENST00000380473.8	NP_689538.1	Q8N6G2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TEX26	ENST00000380473.8 link	c.313-1G>A	splice_acceptor_variant, intron_variant	Intron 3 of 6	1	NM_152325.3	ENSP00000369840.3	Q8N6G2
TEX26	ENST00000531960.1 link	n.138-1G>A	splice_acceptor_variant, intron_variant	Intron 2 of 5	3		ENSP00000435263.1	H0YE92
TEX26	ENST00000530916.1 link	n.-86G>A	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43700

AN:

151896

Hom.:

7486

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.345

AC:

86593

AN:

250808

AF XY:

0.353

show subpopulations

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 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.:

AF XY:

0.368

AC XY:

267235

AN XY:

726220

show subpopulations

African (AFR)

AF:

0.0871

AC:

2913

AN:

33438

American (AMR)

AF:

0.312

AC:

13911

AN:

44592

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

10634

AN:

26106

East Asian (EAS)

AF:

0.267

AC:

10583

AN:

39686

South Asian (SAS)

AF:

0.370

AC:

31885

AN:

86162

European-Finnish (FIN)

AF:

0.397

AC:

21194

AN:

53400

Middle Eastern (MID)

AF:

0.411

AC:

2367

AN:

5754

European-Non Finnish (NFE)

AF:

0.377

AC:

418636

AN:

1110094

Other (OTH)

AF:

0.360

AC:

21696

AN:

60310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

15817

31633

47450

63266

79083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.287

AC:

43703

AN:

152012

Hom.:

7485

Cov.:

AF XY:

0.290

AC XY:

21536

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.0933

AC:

3870

AN:

41470

American (AMR)

AF:

0.299

AC:

4565

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1420

AN:

3468

East Asian (EAS)

AF:

0.284

AC:

1465

AN:

5162

South Asian (SAS)

AF:

0.359

AC:

1727

AN:

4812

European-Finnish (FIN)

AF:

0.402

AC:

4243

AN:

10554

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.374

AC:

25389

AN:

67950

Other (OTH)

AF:

0.330

AC:

696

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1466

2932

4398

5864

7330

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.342

Hom.:

26737

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

BayesDel_noAF

Benign

-0.46

CADD

Uncertain

(source)

DANN

Benign

0.92

Eigen

Uncertain

0.65

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Benign

0.72

PhyloP100

2.9

GERP RS

4.7

Mutation Taster

=73/27

polymorphism (auto)

(source)

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

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rs12857479

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over