rs1969253

Positions:

• chr3-184158724-A-C
• chr3-184158724-A-G
• chr3-184158724-A-T

Variant summary

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

The NM_004423.4(DVL3):​c.161+2928A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,280 control chromosomes in the GnomAD database, including 19,787 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 0.51 (19787 hom., cov: 29)
• Consequence: DVL3 NM_004423.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DVL3	NM_004423.4	c.161+2928A>C		intron_variant		ENST00000313143.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DVL3	ENST00000313143.9	c.161+2928A>C		intron_variant		1	NM_004423.4	P1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 76962 AN: 151170 Hom.: 19755 Cov.: 29

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.509 AC: 77042 AN: 151280 Hom.: 19787 Cov.: 29 AF XY: 0.509 AC XY: 37545 AN XY: 73808

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.500

Alfa AF: 0.520 Hom.: 28133

Bravo AF: 0.501

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.76

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: rs1969253; hg19: chr3-183876512;