chr17-58692120-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.719 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.-183G>C		upstream_gene	N/A	NP_112562.3
	IGBP1C	NM_001395966.1	MANE Select	c.-412G>C		upstream_gene	N/A	NP_001382895.1
	TEX14	NM_001201457.2		c.-183G>C		upstream_gene	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.-183G>C		upstream_gene	N/A	ENSP00000268910.8
	IGBP1C	ENST00000583666.3	TSL:3 MANE Select	c.-412G>C		upstream_gene	N/A	ENSP00000492384.1
	TEX14	ENST00000240361.12	TSL:1	c.-183G>C		upstream_gene	N/A	ENSP00000240361.8

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.222 AC: 105 AN: 472

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 2 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 30

South Asian (SAS) AF: 0.342 AC: 89 AN: 260

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.439 AC: 466 AN: 1062

Other (OTH) AF: 0.438 AC: 28 AN: 64

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

African (AFR) AF: 0.730 AC: 11562 AN: 15834

American (AMR) AF: 0.613 AC: 3143 AN: 5126

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 1553 AN: 2270

East Asian (EAS) AF: 0.550 AC: 928 AN: 1686

South Asian (SAS) AF: 0.634 AC: 978 AN: 1542

European-Finnish (FIN) AF: 0.681 AC: 1957 AN: 2874

Middle Eastern (MID) AF: 0.750 AC: 117 AN: 156

European-Non Finnish (NFE) AF: 0.689 AC: 27105 AN: 39330

Other (OTH) AF: 0.665 AC: 633 AN: 952

Alfa AF: 0.624 Hom.: 2759

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.097
PhyloP100		-1.1
PromoterAI		-0.059	Neutral

Splicing

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

Other links and lift over

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