rs302874

Positions:

• chr17-58690635-A-G
• chr17-58690635-A-T

Variant summary

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

The NM_031272.5(TEX14):​c.-2+1304T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,998 control chromosomes in the GnomAD database, including 29,905 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 0.62 (29905 hom., cov: 31)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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 (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGBP1C	NM_001395966.1	c.-231+1304T>C		intron_variant		ENST00000583666.3
TEX14	NM_031272.5	c.-2+1304T>C		intron_variant		ENST00000349033.10
TEX14	NM_001201457.2	c.-2+1304T>C		intron_variant
TEX14	NM_198393.4	c.-2+1304T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX14	ENST00000349033.10	c.-2+1304T>C		intron_variant		5	NM_031272.5	A2
IGBP1C	ENST00000583666.3	c.-231+1304T>C		intron_variant		3	NM_001395966.1	P1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94584 AN: 151880 Hom.: 29855 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.623 AC: 94684 AN: 151998 Hom.: 29905 Cov.: 31 AF XY: 0.622 AC XY: 46255 AN XY: 74310

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.618

Alfa AF: 0.605 Hom.: 5859

Bravo AF: 0.610

Asia WGS AF: 0.555 AC: 1928 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	3.1
DANN	Benign	0.62

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: rs302874; hg19: chr17-56767996;