rs2084414

Variant names:

• chr8-541735-G-A
• rs2084414
• NM_001384899.1:c.108+2915C>T

Variant summary

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

The NM_001384899.1(TDRP):​c.108+2915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,050 control chromosomes in the GnomAD database, including 42,990 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 0.75 (42990 hom., cov: 32)
• Consequence: TDRP NM_001384899.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 6 publications found

Genes affected

TDRP (HGNC:26951): (testis development related protein) Acts upstream of or within spermatogenesis. Located in cytosol and nucleus. [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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384899.1. 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
	TDRP	NM_001384899.1	MANE Select	c.108+2915C>T		intron	N/A	NP_001371828.1
	TDRP	NM_001256113.2		c.108+2915C>T		intron	N/A	NP_001243042.1
	TDRP	NM_175075.5		c.108+2915C>T		intron	N/A	NP_778250.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TDRP	ENST00000324079.11	TSL:1 MANE Select	c.108+2915C>T		intron	N/A	ENSP00000315111.6
	TDRP	ENST00000523656.5	TSL:5	c.108+2915C>T		intron	N/A	ENSP00000430325.1

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113905 AN: 151932 Hom.: 42933 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.750 AC: 114024 AN: 152050 Hom.: 42990 Cov.: 32 AF XY: 0.742 AC XY: 55138 AN XY: 74326

African (AFR) AF: 0.749 AC: 31047 AN: 41460

American (AMR) AF: 0.802 AC: 12267 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2742 AN: 3472

East Asian (EAS) AF: 0.724 AC: 3736 AN: 5162

South Asian (SAS) AF: 0.765 AC: 3685 AN: 4816

European-Finnish (FIN) AF: 0.570 AC: 6011 AN: 10548

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51938 AN: 67976

Other (OTH) AF: 0.773 AC: 1633 AN: 2112

Alfa AF: 0.768 Hom.: 192765

Bravo AF: 0.765

Asia WGS AF: 0.777 AC: 2704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.39
PhyloP100		0.027
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: rs2084414; hg19: chr8-491735;