rs6980502

Positions:

• chr8-30836637-A-G

Variant summary

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

The NM_001350162.2(TEX15):​c.9481+166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,140 control chromosomes in the GnomAD database, including 1,732 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 0.12 (1732 hom., cov: 31)
• Consequence: TEX15 NM_001350162.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX15	NM_001350162.2	c.9481+166T>C		intron_variant		ENST00000643185.2	NP_001337091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX15	ENST00000643185.2	c.9481+166T>C		intron_variant			NM_001350162.2	ENSP00000493555	P4
TEX15	ENST00000256246.5	c.8332+166T>C		intron_variant		1		ENSP00000256246
TEX15	ENST00000638951.1	c.9493+166T>C		intron_variant		5		ENSP00000492713	A2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17733 AN: 152022 Hom.: 1728 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0519

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.117 AC: 17769 AN: 152140 Hom.: 1732 Cov.: 31 AF XY: 0.115 AC XY: 8583 AN XY: 74410

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.0507

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0519

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0611 Hom.: 820

Bravo AF: 0.122

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6980502; hg19: chr8-30694153;