rs297257

chr10-125620145-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532135.5(TEX36):c.264+40876T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,972 control chromosomes in the GnomAD database, including 19,253 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (19253 hom., cov: 32)
• Consequence: TEX36 ENST00000532135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

TEX36 (HGNC:31653): (testis expressed 36)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX36	NM_001318133.2	c.264+40876T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX36	ENST00000532135.5	c.264+40876T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68872 AN: 151854 Hom.: 19204 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.424

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.454 AC: 68980 AN: 151972 Hom.: 19253 Cov.: 32 AF XY: 0.445 AC XY: 33024 AN XY: 74286

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.426

Alfa AF: 0.393 Hom.: 1862

Bravo AF: 0.481

Asia WGS AF: 0.366 AC: 1269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.41
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs297257; hg19: chr10-127308714;