17-58631697-G-C

Position:

• chr17-58631697-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

U3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TEX14	NM_031272.5	c.137-1143C>G		intron_variant		ENST00000349033.10	NP_112562.3
TEX14	NM_001201457.2	c.137-1143C>G		intron_variant			NP_001188386.1
TEX14	NM_198393.4	c.137-1143C>G		intron_variant			NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.137-1143C>G		intron_variant		5	NM_031272.5	ENSP00000268910	A2
U3	ENST00000390893.2	n.140C>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 FIN exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.501

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

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: rs412000; hg19: chr17-56709058;