17-58680223-G-A

Position:

• chr17-58680223-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.-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

Genes affected

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]

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGBP1C	NM_001395966.1	c.-231+11716C>T		intron_variant		ENST00000583666.3	NP_001382895.1
TEX14	NM_031272.5	c.-2+11716C>T		intron_variant		ENST00000349033.10	NP_112562.3
TEX14	NM_001201457.2	c.-2+11716C>T		intron_variant			NP_001188386.1
TEX14	NM_198393.4	c.-2+11716C>T		intron_variant			NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.-2+11716C>T		intron_variant		5	NM_031272.5	ENSP00000268910	A2
IGBP1C	ENST00000583666.3	c.-231+11716C>T		intron_variant		3	NM_001395966.1	ENSP00000492384	P1

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

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00810

Gnomad4 FIN AF: 0.0543

Gnomad4 NFE AF: 0.0936

Gnomad4 OTH AF: 0.0834

Alfa AF: 0.0899 Hom.: 708

Bravo AF: 0.0619

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.83

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: rs302864; hg19: chr17-56757584;