rs3833528

chr1-151771394-TA-Tchr1-151771394-TA-TAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000525790.5(TDRKH):c.*1203-833del variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.41 (13808 hom., cov: 0)
  • Exomes 𝑓: 0.49 (145765 hom.)
• Consequence: TDRKH ENST00000525790.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

TDRKH (HGNC:11713): (tudor and KH domain containing) Predicted to enable RNA binding activity. Predicted to be involved in fertilization; gamete generation; and piRNA metabolic process. Predicted to be located in mitochondrion; pi-body; and piP-body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TDRKH	XM_017000123.3	c.*40-833del		intron_variant
TDRKH	XM_047441989.1	c.*40-833del		intron_variant
TDRKH	XM_047442008.1	c.*40-833del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TDRKH	ENST00000525790.5	c.*1203-833del		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62268 AN: 151866 Hom.: 13809 Cov.: 0

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.404

GnomAD4 exome AF: 0.490 AC: 583051 AN: 1190756 Hom.: 145765 Cov.: 0 AF XY: 0.488 AC XY: 281328 AN XY: 576552

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.304

Gnomad4 ASJ exome AF: 0.411

Gnomad4 EAS exome AF: 0.244

Gnomad4 SAS exome AF: 0.405

Gnomad4 FIN exome AF: 0.472

Gnomad4 NFE exome AF: 0.515

Gnomad4 OTH exome AF: 0.448

GnomAD4 genome AF: 0.410 AC: 62268 AN: 151984 Hom.: 13808 Cov.: 0 AF XY: 0.404 AC XY: 29989 AN XY: 74296

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.405

Alfa AF: 0.469 Hom.: 2114

Bravo AF: 0.393

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3833528; hg19: chr1-151743870;