Variant 9-97430831-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014290.3(TDRD7):c.208-102T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,399,806 control chromosomes in the GnomAD database, including 143,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 15936 hom., cov: 32)

Exomes 𝑓: 0.45 ( 128017 hom. )

Consequence

TDRD7
NM_014290.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.03

Variant links:

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]

TDRD7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 9-97430831-T-C is Benign according to our data. Variant chr9-97430831-T-C is described in ClinVar as [Benign]. Clinvar id is 1256911.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TDRD7	NM_014290.3 linkuse as main transcript	c.208-102T>C	intron_variant	ENST00000355295.5	NP_055105.2	Q8NHU6-1
TDRD7	NM_001302884.2 linkuse as main transcript	c.-15-102T>C	intron_variant		NP_001289813.1	Q8NHU6-2
TDRD7	XM_047423111.1 linkuse as main transcript	c.208-102T>C	intron_variant		XP_047279067.1
TDRD7	XM_047423113.1 linkuse as main transcript	c.208-102T>C	intron_variant		XP_047279069.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TDRD7	ENST00000355295.5 linkuse as main transcript	c.208-102T>C		intron_variant		1	NM_014290.3	ENSP00000347444.4		Q8NHU6-1

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69407

AN:

151878

Hom.:

15928

Cov.:

show subpopulations

Gnomad AFR

AF:

0.440

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.465

GnomAD4 exome

AF:

0.450

AC:

561955

AN:

1247810

Hom.:

128017

AF XY:

0.447

AC XY:

282147

AN XY:

631704

show subpopulations

Gnomad4 AFR exome

AF:

0.438

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.444

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.360

Gnomad4 FIN exome

AF:

0.453

Gnomad4 NFE exome

AF:

0.455

Gnomad4 OTH exome

AF:

0.443

GnomAD4 genome

AF:

0.457

AC:

69452

AN:

151996

Hom.:

15936

Cov.:

AF XY:

0.457

AC XY:

33927

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.440

Gnomad4 AMR

AF:

0.515

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.360

Gnomad4 FIN

AF:

0.462

Gnomad4 NFE

AF:

0.461

Gnomad4 OTH

AF:

0.463

Alfa

AF:

0.449

Hom.:

3041

Bravo

AF:

0.461

Asia WGS

AF:

0.433

AC:

1508

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over