rs60760897

Variant names:

• chr1-154532373-C-T
• rs60760897
• NM_182499.4:c.370-9651C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

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 = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TDRD10	NM_182499.4	c.370-9651C>T		intron_variant	Intron 6 of 12	ENST00000368482.8	NP_872305.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TDRD10	ENST00000368482.8	c.370-9651C>T		intron_variant	Intron 6 of 12	1	NM_182499.4	ENSP00000357467.4
TDRD10	ENST00000479937.5	n.115-9651C>T		intron_variant	Intron 1 of 7	1
TDRD10	ENST00000368480.3	c.370-9651C>T		intron_variant	Intron 6 of 11	2		ENSP00000357465.3

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

African (AFR) AF: 0.147 AC: 6109 AN: 41522

American (AMR) AF: 0.163 AC: 2498 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3472

East Asian (EAS) AF: 0.156 AC: 803 AN: 5148

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4818

European-Finnish (FIN) AF: 0.351 AC: 3714 AN: 10572

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14104 AN: 67946

Other (OTH) AF: 0.205 AC: 433 AN: 2112

Alfa AF: 0.208 Hom.: 424

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
PhyloP100		-1.3
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: rs60760897; hg19: chr1-154504849; COSMIC: COSV63813637; COSMIC: COSV63813637;