NM_031272.5:c.-183G>C

Variant names:

• chr17-58692120-C-G
• rs302873
• NM_031272.5:c.-183G>C

Variant summary

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

The NM_031272.5(TEX14):​c.-183G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 72,160 control chromosomes in the GnomAD database, including 14,712 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 0.69 (14519 hom., cov: 9)
  • Exomes 𝑓: 0.37 (193 hom.)
• Consequence: TEX14 NM_031272.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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

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 = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX14	NM_031272.5	c.-183G>C		upstream_gene_variant		ENST00000349033.10	NP_112562.3
IGBP1C	NM_001395966.1	c.-412G>C		upstream_gene_variant		ENST00000583666.3	NP_001382895.1
TEX14	NM_001201457.2	c.-183G>C		upstream_gene_variant			NP_001188386.1
TEX14	NM_198393.4	c.-183G>C		upstream_gene_variant			NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.-183G>C		upstream_gene_variant		5	NM_031272.5	ENSP00000268910.8
IGBP1C	ENST00000583666.3	c.-412G>C		upstream_gene_variant		3	NM_001395966.1	ENSP00000492384.1

Frequencies

GnomAD3 genomes AF: 0.687 AC: 48269 AN: 70270 Hom.: 14507 Cov.: 9

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.365 AC: 693 AN: 1898 Hom.: 193 AF XY: 0.386 AC XY: 393 AN XY: 1018

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.222

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.342

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.438

GnomAD4 genome AF: 0.687 AC: 48277 AN: 70262 Hom.: 14519 Cov.: 9 AF XY: 0.684 AC XY: 21786 AN XY: 31850

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.665

Alfa AF: 0.624 Hom.: 2759

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.097

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs302873; hg19: chr17-56769481; COSMIC: COSV53618722;