chr10-114212623-G-A

Variant names:

• chr10-114212623-G-A
• rs10510001
• NM_001395205.1:c.1831+587G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395205.1(TDRD1):​c.1831+587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,004 control chromosomes in the GnomAD database, including 5,118 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 0.25 (5118 hom., cov: 32)
• Consequence: TDRD1 NM_001395205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 1 publications found

Genes affected

TDRD1 (HGNC:11712): (tudor domain containing 1) This gene encodes a protein containing a tudor domain that is thought to function in the suppression of transposable elements during spermatogenesis. The related protein in mouse forms a complex with piRNAs and Piwi proteins to promote methylation and silencing of target sequences. This gene was observed to be upregulated by ETS transcription factor ERG in prostate tumors. [provided by RefSeq, Sep 2018]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TDRD1	NM_001395205.1	MANE Select	c.1831+587G>A		intron	N/A	NP_001382134.1	Q9BXT4-1
	TDRD1	NM_001385363.1		c.1831+587G>A		intron	N/A	NP_001372292.1	Q9BXT4-3
	TDRD1	NM_198795.2		c.1831+587G>A		intron	N/A	NP_942090.1	Q9BXT4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TDRD1	ENST00000695399.1	MANE Select	c.1831+587G>A		intron	N/A	ENSP00000511878.1	Q9BXT4-1
	TDRD1	ENST00000251864.7	TSL:1	c.1831+587G>A		intron	N/A	ENSP00000251864.2	Q9BXT4-3
	TDRD1	ENST00000952550.1		c.1831+587G>A		intron	N/A	ENSP00000622609.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38239 AN: 151886 Hom.: 5097 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.252 AC: 38314 AN: 152004 Hom.: 5118 Cov.: 32 AF XY: 0.249 AC XY: 18527 AN XY: 74302

African (AFR) AF: 0.330 AC: 13660 AN: 41422

American (AMR) AF: 0.222 AC: 3397 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1111 AN: 3470

East Asian (EAS) AF: 0.0728 AC: 377 AN: 5180

South Asian (SAS) AF: 0.128 AC: 615 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2256 AN: 10542

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15981 AN: 67966

Other (OTH) AF: 0.246 AC: 521 AN: 2116

Alfa AF: 0.250 Hom.: 655

Bravo AF: 0.257

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		-0.23
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: rs10510001; hg19: chr10-115972382;