rs1536053

Positions:

• chr13-111329944-C-T

Variant summary

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

The NM_152324.3(TEX29):​c.169+1651C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,806 control chromosomes in the GnomAD database, including 5,654 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 0.27 (5654 hom., cov: 31)
• Consequence: TEX29 NM_152324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

TEX29 (HGNC:20370): (testis expressed 29) Predicted to be integral component of membrane. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX29	NM_152324.3	c.169+1651C>T		intron_variant		ENST00000283547.2	NP_689537.1
TEX29	NM_001303133.1	c.93+1651C>T		intron_variant			NP_001290062.1
TEX29	XM_017020387.2	c.250+1651C>T		intron_variant			XP_016875876.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX29	ENST00000283547.2	c.169+1651C>T		intron_variant		1	NM_152324.3	ENSP00000283547.1
TEX29	ENST00000497241.5	n.250+1651C>T		intron_variant		5		ENSP00000431661.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40382 AN: 151688 Hom.: 5651 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.266 AC: 40395 AN: 151806 Hom.: 5654 Cov.: 31 AF XY: 0.264 AC XY: 19616 AN XY: 74170

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.281

Alfa AF: 0.301 Hom.: 7254

Bravo AF: 0.256

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.76

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: rs1536053; hg19: chr13-111982291;