rs302874

Variant names:

• chr17-58690635-A-G
• rs302874
• NM_031272.5:c.-2+1304T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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 = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX14	NM_031272.5	c.-2+1304T>C		intron_variant	Intron 1 of 31	ENST00000349033.10	NP_112562.3
IGBP1C	NM_001395966.1	c.-231+1304T>C		intron_variant	Intron 1 of 1	ENST00000583666.3	NP_001382895.1
TEX14	NM_001201457.2	c.-2+1304T>C		intron_variant	Intron 1 of 32		NP_001188386.1
TEX14	NM_198393.4	c.-2+1304T>C		intron_variant	Intron 1 of 32		NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10	c.-2+1304T>C		intron_variant	Intron 1 of 31	5	NM_031272.5	ENSP00000268910.8
IGBP1C	ENST00000583666.3	c.-231+1304T>C		intron_variant	Intron 1 of 1	3	NM_001395966.1	ENSP00000492384.1

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

African (AFR) AF: 0.707 AC: 29337 AN: 41476

American (AMR) AF: 0.514 AC: 7837 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2531 AN: 5166

South Asian (SAS) AF: 0.587 AC: 2835 AN: 4826

European-Finnish (FIN) AF: 0.629 AC: 6634 AN: 10552

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41453 AN: 67938

Other (OTH) AF: 0.618 AC: 1306 AN: 2112

Alfa AF: 0.601 Hom.: 9111

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
PhyloP100		-0.020
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs302874; hg19: chr17-56767996;