NM_031272.5:c.-2+11716C>T

Variant names:

• chr17-58680223-G-A
• rs302864
• NM_031272.5:c.-2+11716C>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.-2+11716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,052 control chromosomes in the GnomAD database, including 414 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 0.061 (414 hom., cov: 32)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 16 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]

IGBP1C (HGNC:43611): (IGBP1 family member C) Predicted to enable protein phosphatase 2A binding activity. Predicted to be involved in regulation of dephosphorylation. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0916 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.-2+11716C>T		intron	N/A	NP_112562.3
	IGBP1C	NM_001395966.1	MANE Select	c.-231+11716C>T		intron	N/A	NP_001382895.1
	TEX14	NM_001201457.2		c.-2+11716C>T		intron	N/A	NP_001188386.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX14	ENST00000349033.10	TSL:5 MANE Select	c.-2+11716C>T		intron	N/A	ENSP00000268910.8
	IGBP1C	ENST00000583666.3	TSL:3 MANE Select	c.-231+11716C>T		intron	N/A	ENSP00000492384.1
	TEX14	ENST00000240361.12	TSL:1	c.-2+11716C>T		intron	N/A	ENSP00000240361.8

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9260 AN: 151934 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00789

Gnomad FIN AF: 0.0543

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0609 AC: 9254 AN: 152052 Hom.: 414 Cov.: 32 AF XY: 0.0582 AC XY: 4322 AN XY: 74314

African (AFR) AF: 0.0171 AC: 708 AN: 41478

American (AMR) AF: 0.0686 AC: 1046 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5172

South Asian (SAS) AF: 0.00810 AC: 39 AN: 4812

European-Finnish (FIN) AF: 0.0543 AC: 575 AN: 10582

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6360 AN: 67976

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0865 Hom.: 834

Bravo AF: 0.0619

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.83
PhyloP100		-1.0
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: rs302864; hg19: chr17-56757584;