NM_031272.5:c.1184+2068C>T

Variant names:

• chr17-58609093-G-A
• rs302848
• NM_031272.5:c.1184+2068C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031272.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX14	NM_031272.5	MANE Select	c.1184+2068C>T		intron	N/A	NP_112562.3
	TEX14	NM_001201457.2		c.1202+2068C>T		intron	N/A	NP_001188386.1
	TEX14	NM_198393.4		c.1184+2068C>T		intron	N/A	NP_938207.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX14	ENST00000349033.10	TSL:5 MANE Select	c.1184+2068C>T		intron	N/A	ENSP00000268910.8
	TEX14	ENST00000240361.12	TSL:1	c.1202+2068C>T		intron	N/A	ENSP00000240361.8
	TEX14	ENST00000389934.7	TSL:1	c.1184+2068C>T		intron	N/A	ENSP00000374584.3

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

African (AFR) AF: 0.711 AC: 29503 AN: 41484

American (AMR) AF: 0.522 AC: 7961 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2126 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2533 AN: 5148

South Asian (SAS) AF: 0.614 AC: 2962 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6925 AN: 10554

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42756 AN: 67978

Other (OTH) AF: 0.633 AC: 1333 AN: 2106

Alfa AF: 0.618 Hom.: 39451

Bravo AF: 0.621

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.37
PhyloP100		-0.35
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: rs302848; hg19: chr17-56686454;