3-184163446-G-A

Variant summary

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

The NM_004423.4(DVL3):c.162-211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,182 control chromosomes in the GnomAD database, including 1,202 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (1202 hom., cov: 31)
• Consequence: DVL3 NM_004423.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.454

Genes affected

DVL3 (HGNC:3087): (dishevelled segment polarity protein 3) This gene is a member of a multi-gene family which shares strong similarity with the Drosophila dishevelled gene, dsh. The Drosophila dishevelled gene encodes a cytoplasmic phosphoprotein that regulates cell proliferation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 3-184163446-G-A is Benign according to our data. Variant chr3-184163446-G-A is described in ClinVar as [Benign]. Clinvar id is 1222819.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DVL3	NM_004423.4	c.162-211G>A		intron_variant		ENST00000313143.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DVL3	ENST00000313143.9	c.162-211G>A		intron_variant		1	NM_004423.4	P1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17007 AN: 152064 Hom.: 1204 Cov.: 31

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.112 AC: 17014 AN: 152182 Hom.: 1202 Cov.: 31 AF XY: 0.110 AC XY: 8160 AN XY: 74414

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00502

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.108

Alfa AF: 0.144 Hom.: 405

Bravo AF: 0.105

Asia WGS AF: 0.0820 AC: 284 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

Dec 01, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.0
Dann	Benign	0.71

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: rs73185718; hg19: chr3-183881234;