chr17-58631673-G-A

Variant names:

• chr17-58631673-G-A
• rs411988
• NM_031272.5:c.137-1119C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_031272.5(TEX14):​c.137-1119C>T 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 150,590 control chromosomes in the GnomAD database, including 18,337 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 (18336 hom., cov: 29)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 31 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• 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.137-1119C>T		intron_variant	Intron 2 of 31	ENST00000349033.10	NP_112562.3
LOC124904154		n.58631673G>A		intragenic_variant
TEX14	NM_001201457.2	c.137-1119C>T		intron_variant	Intron 2 of 32		NP_001188386.1
TEX14	NM_198393.4	c.137-1119C>T		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.137-1119C>T		intron_variant	Intron 2 of 31	5	NM_031272.5	ENSP00000268910.8

Frequencies

GnomAD3 genomes AF: 0.484 AC: 72887 AN: 150506 Hom.: 18320 Cov.: 29

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.507

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

GnomAD4 genome AF: 0.484 AC: 72938 AN: 150586 Hom.: 18336 Cov.: 29 AF XY: 0.481 AC XY: 35329 AN XY: 73402

African (AFR) AF: 0.410 AC: 16797 AN: 40998

American (AMR) AF: 0.439 AC: 6642 AN: 15120

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

East Asian (EAS) AF: 0.180 AC: 923 AN: 5134

South Asian (SAS) AF: 0.335 AC: 1604 AN: 4782

European-Finnish (FIN) AF: 0.565 AC: 5692 AN: 10068

Middle Eastern (MID) AF: 0.572 AC: 166 AN: 290

European-Non Finnish (NFE) AF: 0.557 AC: 37758 AN: 67738

Other (OTH) AF: 0.503 AC: 1047 AN: 2082

Alfa AF: 0.514 Hom.: 2762

Bravo AF: 0.466

Asia WGS AF: 0.263 AC: 916 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	6.3
DANN	Benign	0.76
PhyloP100		1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		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: rs411988; hg19: chr17-56709034;