rs323376

Positions:

• chr8-30874013-C-A
• chr8-30874013-C-T

Variant summary

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

The NM_001350162.2(TEX15):​c.302+924G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,034 control chromosomes in the GnomAD database, including 15,065 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 0.36 (15065 hom., cov: 32)
• Consequence: TEX15 NM_001350162.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

Genes affected

TEX15 (HGNC:11738): (testis expressed 15, meiosis and synapsis associated) This gene encodes a protein that is required for DNA double-strand break repair, chromosome synapsis, and meiotic recombination in spermatocytes. Male mice with a knockout of the orthologous gene are viable but sterile. Loss-of-function mutations in the orthologous mouse gene cause early meiotic arrest in spermatocytes, before the mid-pachytene stage. Naturally occurring mutations in this gene are associated with nonobstructive azoospermia. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX15	NM_001350162.2	c.302+924G>T		intron_variant		ENST00000643185.2	NP_001337091.1
TEX15	NR_146525.2	n.382+924G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX15	ENST00000643185.2	c.302+924G>T		intron_variant			NM_001350162.2	ENSP00000493555	P4
TEX15	ENST00000638951.1	c.314+924G>T		intron_variant		5		ENSP00000492713	A2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54519 AN: 151916 Hom.: 15027 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.0782

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.359 AC: 54623 AN: 152034 Hom.: 15065 Cov.: 32 AF XY: 0.358 AC XY: 26640 AN XY: 74324

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.317

Alfa AF: 0.175 Hom.: 836

Bravo AF: 0.384

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs323376; hg19: chr8-30731529;