17-58631697-G-C

Variant names:

• chr17-58631697-G-C
• rs412000
• NM_031272.5:c.137-1143C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031272.5(TEX14):​c.137-1143C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,170 control chromosomes in the GnomAD database, including 18,376 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 0.48 (18374 hom., cov: 30)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 22 publications found

Genes affected

TEX14 (HGNC:11737): (testis expressed 14, intercellular bridge forming factor) The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

TEX14 Gene-Disease associations (from GenCC):

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

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

U3 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX14	NM_031272.5	c.137-1143C>G		intron_variant	Intron 2 of 31	ENST00000349033.10	NP_112562.3
LOC124904154		n.58631697G>C		intragenic_variant
TEX14	NM_001201457.2	c.137-1143C>G		intron_variant	Intron 2 of 32		NP_001188386.1
TEX14	NM_198393.4	c.137-1143C>G		intron_variant	Intron 2 of 32		NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.137-1143C>G		intron_variant	Intron 2 of 31	5	NM_031272.5	ENSP00000268910.8

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73058 AN: 151072 Hom.: 18357 Cov.: 30

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.484 AC: 73112 AN: 151164 Hom.: 18374 Cov.: 30 AF XY: 0.480 AC XY: 35450 AN XY: 73792

African (AFR) AF: 0.409 AC: 16811 AN: 41118

American (AMR) AF: 0.438 AC: 6664 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3466

East Asian (EAS) AF: 0.180 AC: 926 AN: 5140

South Asian (SAS) AF: 0.335 AC: 1606 AN: 4796

European-Finnish (FIN) AF: 0.560 AC: 5782 AN: 10320

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.557 AC: 37798 AN: 67830

Other (OTH) AF: 0.501 AC: 1049 AN: 2092

Alfa AF: 0.246 Hom.: 387

Bravo AF: 0.466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.99
DANN	Benign	0.48
PhyloP100		0.073
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: rs412000; hg19: chr17-56709058;