dbSNP rs16920147: TDRD7:c.207+19G>A (chr9-97428691-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

1 publications found

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 Gene-Disease associations (from GenCC):

cataract 36
Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P

TDRD7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014290.3. 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
	TDRD7	NM_014290.3	MANE Select	c.207+19G>A		intron	N/A	NP_055105.2	Q8NHU6-1
	TDRD7	NM_001302884.2		c.-15-2242G>A		intron	N/A	NP_001289813.1	Q8NHU6-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TDRD7	ENST00000355295.5	TSL:1 MANE Select	c.207+19G>A	intron	N/A	ENSP00000347444.4	Q8NHU6-1
TDRD7	ENST00000861598.1		c.207+19G>A	intron	N/A	ENSP00000531657.1
TDRD7	ENST00000861599.1		c.207+19G>A	intron	N/A	ENSP00000531658.1

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

GnomAD2 exomes

AF:

0.0169

AC:

4204

AN:

248692

AF XY:

0.0177

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 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

African (AFR)

AF:

0.000569

AC:

AN:

33384

American (AMR)

AF:

0.00190

AC:

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.00774

AC:

202

AN:

26108

East Asian (EAS)

AF:

0.0854

AC:

3389

AN:

39676

South Asian (SAS)

AF:

0.0433

AC:

3732

AN:

86192

European-Finnish (FIN)

AF:

0.0202

AC:

1035

AN:

51330

Middle Eastern (MID)

AF:

0.00284

AC:

AN:

5634

European-Non Finnish (NFE)

AF:

0.00118

AC:

1308

AN:

1109822

Other (OTH)

AF:

0.0114

AC:

690

AN:

60264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

564

1128

1691

2255

2819

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

142

284

426

568

710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00793

AC:

1208

AN:

152286

Hom.:

Cov.:

AF XY:

0.0101

AC XY:

754

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.000794

AC:

AN:

41562

American (AMR)

AF:

0.00196

AC:

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00894

AC:

AN:

3468

East Asian (EAS)

AF:

0.104

AC:

539

AN:

5184

South Asian (SAS)

AF:

0.0427

AC:

206

AN:

4830

European-Finnish (FIN)

AF:

0.0246

AC:

261

AN:

10604

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00138

AC:

AN:

68030

Other (OTH)

AF:

0.00664

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

109

163

218

272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00250

Hom.:

Bravo

AF:

0.00621

Asia WGS

AF:

0.0600

AC:

207

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Cataract 36 (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.24

(source)

DANN

Benign

0.84

PhyloP100

-2.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over