chr17-58567455-T-C

Position:

• chr17-58567455-T-C

Variant summary

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

The NM_031272.5(TEX14):​c.3887-1631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,174 control chromosomes in the GnomAD database, including 199 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 0.042 (199 hom., cov: 32)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX14	NM_031272.5	c.3887-1631A>G		intron_variant		ENST00000349033.10	NP_112562.3
TEX14	NM_001201457.2	c.4025-1631A>G		intron_variant			NP_001188386.1
TEX14	NM_198393.4	c.4007-1631A>G		intron_variant			NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.3887-1631A>G		intron_variant		5	NM_031272.5	ENSP00000268910	A2

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6373 AN: 152056 Hom.: 198 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0419 AC: 6372 AN: 152174 Hom.: 199 Cov.: 32 AF XY: 0.0415 AC XY: 3085 AN XY: 74398

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0525

Gnomad4 FIN AF: 0.0641

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0553 Hom.: 354

Bravo AF: 0.0360

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.45

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: rs12944693; hg19: chr17-56644816;