Variant 13-59666357-C-CAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001042517.2(DIAPH3):c.*225_*226dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.044 ( 242 hom., cov: 0)

Exomes 𝑓: 0.017 ( 0 hom. )

Consequence

DIAPH3
NM_001042517.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.612

Variant links:

Genes affected

DIAPH3 (HGNC:15480): (diaphanous related formin 3) This gene encodes a member of the diaphanous subfamily of the formin family. Members of this family are involved in actin remodeling and regulate cell movement and adhesion. Mutations in this gene are associated with autosomal dominant auditory neuropathy 1. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

DIAPH3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 13-59666357-C-CAA is Benign according to our data. Variant chr13-59666357-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1225244.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIAPH3	NM_001042517.2 link	c.225_226dupTT		3_prime_UTR_variant	28/28	ENST00000400324.9	NP_001035982.1	Q9NSV4-3B4DPV3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIAPH3	ENST00000400324 link	c.225_226dupTT		3_prime_UTR_variant	28/28	1	NM_001042517.2	ENSP00000383178.3		Q9NSV4-3
DIAPH3	ENST00000649952.1 link	n.671_672dupTT		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.0442

AC:

4945

AN:

111828

Hom.:

240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.00364

Gnomad AMR

AF:

0.0247

Gnomad ASJ

AF:

0.0363

Gnomad EAS

AF:

0.0402

Gnomad SAS

AF:

0.0429

Gnomad FIN

AF:

0.00351

Gnomad MID

AF:

0.0221

Gnomad NFE

AF:

0.00835

Gnomad OTH

AF:

0.0475

GnomAD4 exome

AF:

0.0172

AC:

3247

AN:

189210

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1725

AN XY:

99628

show subpopulations

Gnomad4 AFR exome

AF:

0.0438

Gnomad4 AMR exome

AF:

0.0158

Gnomad4 ASJ exome

AF:

0.0228

Gnomad4 EAS exome

AF:

0.0172

Gnomad4 SAS exome

AF:

0.0242

Gnomad4 FIN exome

AF:

0.0121

Gnomad4 NFE exome

AF:

0.0152

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.0443

AC:

4952

AN:

111808

Hom.:

242

Cov.:

AF XY:

0.0443

AC XY:

2332

AN XY:

52624

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.0247

Gnomad4 ASJ

AF:

0.0363

Gnomad4 EAS

AF:

0.0398

Gnomad4 SAS

AF:

0.0429

Gnomad4 FIN

AF:

0.00351

Gnomad4 NFE

AF:

0.00835

Gnomad4 OTH

AF:

0.0471

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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