9-97430704-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014290.3(TDRD7):c.208-229T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,156 control chromosomes in the GnomAD database, including 4,771 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (4771 hom., cov: 32)
• Consequence: TDRD7 NM_014290.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.493

Genes affected

TDRD7 (HGNC:30831): (tudor domain containing 7) The protein encoded by this gene belongs to the Tudor family of proteins. This protein contains conserved Tudor domains and LOTUS domains. It is a component of RNA granules, which function in RNA processing. Mutations in this gene have been associated with cataract formation in mouse and human. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 9-97430704-T-C is Benign according to our data. Variant chr9-97430704-T-C is described in ClinVar as [Benign]. Clinvar id is 1238760.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TDRD7	NM_014290.3	c.208-229T>C		intron_variant		ENST00000355295.5
TDRD7	NM_001302884.2	c.-15-229T>C		intron_variant
TDRD7	XM_047423111.1	c.208-229T>C		intron_variant
TDRD7	XM_047423113.1	c.208-229T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TDRD7	ENST00000355295.5	c.208-229T>C		intron_variant		1	NM_014290.3	P1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37563 AN: 152038 Hom.: 4775 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37555 AN: 152156 Hom.: 4771 Cov.: 32 AF XY: 0.244 AC XY: 18184 AN XY: 74376

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.258

Alfa AF: 0.271 Hom.: 7518

Bravo AF: 0.246

Asia WGS AF: 0.192 AC: 673 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	9.6
Dann	Benign	0.89

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: rs13286028; hg19: chr9-100192986;