chr13-60016443-A-C

Variant names:

• chr13-60016443-A-C
• rs73214504
• NM_001042517.2:c.627-298T>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001042517.2(DIAPH3):​c.627-298T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 152,174 control chromosomes in the GnomAD database, including 409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.070 (409 hom., cov: 32)
• Consequence: DIAPH3 NM_001042517.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.346

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-AS1 (HGNC:39915): (DIAPH3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 13-60016443-A-C is Benign according to our data. Variant chr13-60016443-A-C is described in ClinVar as [Benign]. Clinvar id is 1282353.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIAPH3	NM_001042517.2	c.627-298T>G		intron_variant	Intron 5 of 27	ENST00000400324.9	NP_001035982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIAPH3	ENST00000400324.9	c.627-298T>G		intron_variant	Intron 5 of 27	1	NM_001042517.2	ENSP00000383178.3
DIAPH3	ENST00000400319.5	c.417-298T>G		intron_variant	Intron 3 of 25	1		ENSP00000383173.1

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10618 AN: 152056 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.0573

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

GnomAD4 genome AF: 0.0698 AC: 10625 AN: 152174 Hom.: 409 Cov.: 32 AF XY: 0.0705 AC XY: 5245 AN XY: 74406

Gnomad4 AFR AF: 0.0944

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.0543

Gnomad4 FIN AF: 0.0657

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.0562

Alfa AF: 0.0345 Hom.: 30

Bravo AF: 0.0736

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.60

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: rs73214504; hg19: chr13-60590577;