rs6980502

Variant names:

• chr8-30836637-A-G
• rs6980502
• NM_001350162.2:c.9481+166T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

TEX15 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• spermatogenic failure 25

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEX15	NM_001350162.2	c.9481+166T>C		intron_variant	Intron 10 of 10	ENST00000643185.2	NP_001337091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX15	ENST00000643185.2	c.9481+166T>C		intron_variant	Intron 10 of 10		NM_001350162.2	ENSP00000493555.1
TEX15	ENST00000256246.5	c.8332+166T>C		intron_variant	Intron 3 of 3	1		ENSP00000256246.2
TEX15	ENST00000638951.1	c.9493+166T>C		intron_variant	Intron 9 of 9	5		ENSP00000492713.1

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

African (AFR) AF: 0.268 AC: 11099 AN: 41470

American (AMR) AF: 0.0632 AC: 966 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3466

East Asian (EAS) AF: 0.0507 AC: 263 AN: 5184

South Asian (SAS) AF: 0.153 AC: 737 AN: 4818

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0519 AC: 3532 AN: 68002

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.0702 Hom.: 2674

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
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6980502; hg19: chr8-30694153;