rs12740969

chr1-154514584-T-G

Variant summary

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

The NM_182499.4(TDRD10):c.142-5720T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,996 control chromosomes in the GnomAD database, including 22,593 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 0.51 (22593 hom., cov: 31)
• Consequence: TDRD10 NM_182499.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

Genes affected

TDRD10 (HGNC:25316): (tudor domain containing 10) Predicted to enable RNA binding activity. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TDRD10	NM_182499.4	c.142-5720T>G		intron_variant		ENST00000368482.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TDRD10	ENST00000368482.8	c.142-5720T>G		intron_variant		1	NM_182499.4	P1
TDRD10	ENST00000368480.3	c.142-5720T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76884 AN: 151878 Hom.: 22590 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.506 AC: 76893 AN: 151996 Hom.: 22593 Cov.: 31 AF XY: 0.506 AC XY: 37585 AN XY: 74308

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.554

Alfa AF: 0.544 Hom.: 3060

Bravo AF: 0.512

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.9
Dann	Benign	0.68

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: rs12740969; hg19: chr1-154487060;