9-97428841-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.207+169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,114 control chromosomes in the GnomAD database, including 15,904 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (15904 hom., cov: 33)
• Consequence: TDRD7 NM_014290.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0520

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=-0.87).
• BP6: Variant 9-97428841-T-C is Benign according to our data. Variant chr9-97428841-T-C is described in ClinVar as [Benign]. Clinvar id is 1260120.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TDRD7	NM_014290.3	c.207+169T>C		intron_variant		ENST00000355295.5
TDRD7	NM_001302884.2	c.-15-2092T>C		intron_variant
TDRD7	XM_047423111.1	c.207+169T>C		intron_variant
TDRD7	XM_047423113.1	c.207+169T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TDRD7	ENST00000355295.5	c.207+169T>C		intron_variant		1	NM_014290.3	P1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69345 AN: 151996 Hom.: 15898 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.456 AC: 69383 AN: 152114 Hom.: 15904 Cov.: 33 AF XY: 0.456 AC XY: 33891 AN XY: 74372

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.462

Alfa AF: 0.453 Hom.: 1899

Bravo AF: 0.461

Asia WGS AF: 0.429 AC: 1493 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 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.79

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: rs60564655; hg19: chr9-100191123;