13-60096113-C-T

Position:

• chr13-60096113-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042517.2(DIAPH3):​c.391-2381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,056 control chromosomes in the GnomAD database, including 459 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.063 (459 hom., cov: 32)
• Consequence: DIAPH3 NM_001042517.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIAPH3	NM_001042517.2	c.391-2381G>A		intron_variant		ENST00000400324.9	NP_001035982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIAPH3	ENST00000400324.9	c.391-2381G>A		intron_variant		1	NM_001042517.2	ENSP00000383178.3
DIAPH3	ENST00000400319.5	c.181-2381G>A		intron_variant		1		ENSP00000383173.1

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9632 AN: 151940 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0710

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0634 AC: 9636 AN: 152056 Hom.: 459 Cov.: 32 AF XY: 0.0633 AC XY: 4702 AN XY: 74320

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.0498

Gnomad4 FIN AF: 0.0710

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.0655

Alfa AF: 0.0595 Hom.: 42

Bravo AF: 0.0613

Asia WGS AF: 0.143 AC: 496 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.42

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: rs10507647; hg19: chr13-60670247;