rs12946522

chr17-58690742-T-G

Variant summary

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

The NM_031272.5(TEX14):c.-2+1197A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,134 control chromosomes in the GnomAD database, including 2,369 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 0.17 (2369 hom., cov: 31)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGBP1C	NM_001395966.1	c.-231+1197A>C		intron_variant		ENST00000583666.3
TEX14	NM_031272.5	c.-2+1197A>C		intron_variant		ENST00000349033.10
TEX14	NM_001201457.2	c.-2+1197A>C		intron_variant
TEX14	NM_198393.4	c.-2+1197A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX14	ENST00000349033.10	c.-2+1197A>C		intron_variant		5	NM_031272.5	A2
IGBP1C	ENST00000583666.3	c.-231+1197A>C		intron_variant		3	NM_001395966.1	P1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26074 AN: 152016 Hom.: 2366 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.172 AC: 26093 AN: 152134 Hom.: 2369 Cov.: 31 AF XY: 0.175 AC XY: 12982 AN XY: 74388

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0777

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.153

Alfa AF: 0.174 Hom.: 3195

Bravo AF: 0.159

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.75
Dann	Benign	0.48

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: rs12946522; hg19: chr17-56768103;