17-58609093-G-A

Position:

• chr17-58609093-G-A

Variant summary

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

The NM_031272.5(TEX14):​c.1184+2068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,032 control chromosomes in the GnomAD database, including 31,199 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 0.64 (31199 hom., cov: 32)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX14	NM_031272.5	c.1184+2068C>T		intron_variant		ENST00000349033.10
TEX14	NM_001201457.2	c.1202+2068C>T		intron_variant
TEX14	NM_198393.4	c.1184+2068C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX14	ENST00000349033.10	c.1184+2068C>T		intron_variant		5	NM_031272.5	A2
TEX14	ENST00000240361.12	c.1202+2068C>T		intron_variant		1		A2
TEX14	ENST00000389934.7	c.1184+2068C>T		intron_variant		1		P4
TEX14	ENST00000582740.1	c.*1022+2068C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96729 AN: 151914 Hom.: 31150 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.637 AC: 96827 AN: 152032 Hom.: 31199 Cov.: 32 AF XY: 0.637 AC XY: 47299 AN XY: 74296

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.633

Alfa AF: 0.619 Hom.: 30359

Bravo AF: 0.621

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.37

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: rs302848; hg19: chr17-56686454;