1-151789328-A-G

Variant names:

• chr1-151789328-A-G
• rs868866
• NM_001083965.2:c.-28+1052T>C

Variant summary

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

The NM_001083965.2(TDRKH):​c.-28+1052T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,148 control chromosomes in the GnomAD database, including 13,495 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 0.41 (13495 hom., cov: 33)
• Consequence: TDRKH NM_001083965.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TDRKH	NM_001083965.2	c.-28+1052T>C		intron_variant	Intron 1 of 12	ENST00000368824.8	NP_001077434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TDRKH	ENST00000368824.8	c.-28+1052T>C		intron_variant	Intron 1 of 12	1	NM_001083965.2	ENSP00000357815.3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61881 AN: 152030 Hom.: 13495 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.407 AC: 61885 AN: 152148 Hom.: 13495 Cov.: 33 AF XY: 0.401 AC XY: 29795 AN XY: 74364

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.406

Alfa AF: 0.365 Hom.: 1581

Bravo AF: 0.389

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.62

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: rs868866; hg19: chr1-151761804;