rs1536053

Variant names:

• chr13-111329944-C-T
• rs1536053
• NM_152324.3:c.169+1651C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEX29	NM_152324.3	c.169+1651C>T		intron_variant	Intron 3 of 5	ENST00000283547.2	NP_689537.1
TEX29	NM_001303133.1	c.93+1651C>T		intron_variant	Intron 3 of 6		NP_001290062.1
TEX29	XM_017020387.2	c.250+1651C>T		intron_variant	Intron 3 of 5		XP_016875876.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX29	ENST00000283547.2	c.169+1651C>T		intron_variant	Intron 3 of 5	1	NM_152324.3	ENSP00000283547.1
TEX29	ENST00000497241.5	n.250+1651C>T		intron_variant	Intron 3 of 6	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

African (AFR) AF: 0.189 AC: 7827 AN: 41352

American (AMR) AF: 0.247 AC: 3772 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1215 AN: 3470

East Asian (EAS) AF: 0.0494 AC: 255 AN: 5166

South Asian (SAS) AF: 0.354 AC: 1703 AN: 4814

European-Finnish (FIN) AF: 0.290 AC: 3051 AN: 10520

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21653 AN: 67926

Other (OTH) AF: 0.281 AC: 590 AN: 2102

Alfa AF: 0.289 Hom.: 11316

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
PhyloP100		0.30
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: rs1536053; hg19: chr13-111982291;