13-59666357-C-CA

Position:

• chr13-59666357-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001042517.2(DIAPH3):​c.*226dupT 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 0.59 (17401 hom., cov: 0)
  • Exomes 𝑓: 0.24 (39 hom.)
• Consequence: DIAPH3 NM_001042517.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.612

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-59666357-C-CA is Benign according to our data. Variant chr13-59666357-C-CA is described in ClinVar as [Benign]. Clinvar id is 1282927.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIAPH3	NM_001042517.2	c.*226dupT		3_prime_UTR_variant	28/28	ENST00000400324.9	NP_001035982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIAPH3	ENST00000400324	c.*226dupT		3_prime_UTR_variant	28/28	1	NM_001042517.2	ENSP00000383178.3
DIAPH3	ENST00000649952.1	n.672dupT		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.593 AC: 66325 AN: 111846 Hom.: 17407 Cov.: 0

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.241 AC: 45553 AN: 189138 Hom.: 39 Cov.: 0 AF XY: 0.239 AC XY: 23822 AN XY: 99600

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.239

Gnomad4 EAS exome AF: 0.203

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.271

Gnomad4 NFE exome AF: 0.247

Gnomad4 OTH exome AF: 0.234

GnomAD4 genome AF: 0.593 AC: 66307 AN: 111830 Hom.: 17401 Cov.: 0 AF XY: 0.591 AC XY: 31124 AN XY: 52622

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.553

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

Aug 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs11421911; hg19: chr13-60240491;