rs2725854

chr15-56285633-C-T

Variant summary

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

The NM_001385040.1(TEX9):c.-43+41355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,950 control chromosomes in the GnomAD database, including 10,524 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 0.35 (10524 hom., cov: 32)
• Consequence: TEX9 NM_001385040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

Genes affected

TEX9 (HGNC:29585): (testis expressed 9)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX9	NM_001385040.1	c.-43+41355C>T		intron_variant
TEX9	NM_001385041.1	c.-168+41355C>T		intron_variant
TEX9	NM_001385042.1	c.-107+41355C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX9	ENST00000560827.6	c.-107+41355C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52753 AN: 151832 Hom.: 10528 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.347 AC: 52756 AN: 151950 Hom.: 10524 Cov.: 32 AF XY: 0.347 AC XY: 25786 AN XY: 74242

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.338

Alfa AF: 0.409 Hom.: 5996

Bravo AF: 0.334

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2725854; hg19: chr15-56577831;