Variant 9-97428691-G-A 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.207+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00726 in 1,609,366 control chromosomes in the GnomAD database, including 369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0079 ( 40 hom., cov: 33)

Exomes 𝑓: 0.0072 ( 329 hom. )

Consequence

TDRD7
NM_014290.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.81

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 9-97428691-G-A is Benign according to our data. Variant chr9-97428691-G-A is described in ClinVar as [Benign]. Clinvar id is 260380.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TDRD7	NM_014290.3 linkuse as main transcript	c.207+19G>A	intron_variant	ENST00000355295.5	NP_055105.2	Q8NHU6-1
TDRD7	NM_001302884.2 linkuse as main transcript	c.-15-2242G>A	intron_variant		NP_001289813.1	Q8NHU6-2
TDRD7	XM_047423111.1 linkuse as main transcript	c.207+19G>A	intron_variant		XP_047279067.1
TDRD7	XM_047423113.1 linkuse as main transcript	c.207+19G>A	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.207+19G>A		intron_variant		1	NM_014290.3	ENSP00000347444.4		Q8NHU6-1

Frequencies

GnomAD3 genomes

AF:

0.00792

AC:

1205

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000796

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00196

Gnomad ASJ

AF:

0.00894

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0426

Gnomad FIN

AF:

0.0246

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00137

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.0169

AC:

4204

AN:

248692

Hom.:

170

AF XY:

0.0177

AC XY:

2385

AN XY:

134620

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00212

Gnomad ASJ exome

AF:

0.00666

Gnomad EAS exome

AF:

0.109

Gnomad SAS exome

AF:

0.0429

Gnomad FIN exome

AF:

0.0206

Gnomad NFE exome

AF:

0.00239

Gnomad OTH exome

AF:

0.0104

GnomAD4 exome

AF:

0.00719

AC:

10476

AN:

1457080

Hom.:

329

Cov.:

AF XY:

0.00824

AC XY:

5977

AN XY:

725088

show subpopulations

Gnomad4 AFR exome

AF:

0.000569

Gnomad4 AMR exome

AF:

0.00190

Gnomad4 ASJ exome

AF:

0.00774

Gnomad4 EAS exome

AF:

0.0854

Gnomad4 SAS exome

AF:

0.0433

Gnomad4 FIN exome

AF:

0.0202

Gnomad4 NFE exome

AF:

0.00118

Gnomad4 OTH exome

AF:

0.0114

GnomAD4 genome

AF:

0.00793

AC:

1208

AN:

152286

Hom.:

Cov.:

AF XY:

0.0101

AC XY:

754

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.00196

Gnomad4 ASJ

AF:

0.00894

Gnomad4 EAS

AF:

0.104

Gnomad4 SAS

AF:

0.0427

Gnomad4 FIN

AF:

0.0246

Gnomad4 NFE

AF:

0.00138

Gnomad4 OTH

AF:

0.00664

Alfa

AF:

0.00262

Hom.:

Bravo

AF:

0.00621

Asia WGS

AF:

0.0600

AC:

207

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

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	Jan 23, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Cataract 36

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 15, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.24

DANN

Benign

0.84

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

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