rs60760897

Positions:

• chr1-154532373-C-T

Variant summary

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

The NM_182499.4(TDRD10):​c.370-9651C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,096 control chromosomes in the GnomAD database, including 3,107 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 0.19 (3107 hom., cov: 32)
• Consequence: TDRD10 NM_182499.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TDRD10	NM_182499.4	c.370-9651C>T		intron_variant		ENST00000368482.8	NP_872305.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TDRD10	ENST00000368482.8	c.370-9651C>T		intron_variant		1	NM_182499.4	ENSP00000357467	P1
TDRD10	ENST00000479937.5	n.115-9651C>T		intron_variant, non_coding_transcript_variant		1
TDRD10	ENST00000368480.3	c.370-9651C>T		intron_variant		2		ENSP00000357465

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29560 AN: 151978 Hom.: 3103 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.195 AC: 29588 AN: 152096 Hom.: 3107 Cov.: 32 AF XY: 0.201 AC XY: 14963 AN XY: 74334

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.205

Alfa AF: 0.211 Hom.: 416

Bravo AF: 0.175

Asia WGS AF: 0.217 AC: 752 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	3.4
DANN	Benign	0.61

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: rs60760897; hg19: chr1-154504849; COSMIC: COSV63813637; COSMIC: COSV63813637;