rs2504789

Positions:

• chr6-39866538-A-G

Variant summary

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

The NM_001201427.2(DAAM2):​c.429-972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,114 control chromosomes in the GnomAD database, including 29,386 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 0.62 (29386 hom., cov: 33)
• Consequence: DAAM2 NM_001201427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

DAAM2 (HGNC:18143): (dishevelled associated activator of morphogenesis 2) Predicted to enable actin binding activity and small GTPase binding activity. Predicted to be involved in nervous system development and regulation of Wnt signaling pathway. Predicted to act upstream of or within determination of left/right symmetry. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAAM2	NM_001201427.2	c.429-972A>G		intron_variant		ENST00000274867.9	NP_001188356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAAM2	ENST00000274867.9	c.429-972A>G		intron_variant		1	NM_001201427.2	ENSP00000274867	P1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94056 AN: 151996 Hom.: 29366 Cov.: 33

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.619 AC: 94117 AN: 152114 Hom.: 29386 Cov.: 33 AF XY: 0.620 AC XY: 46085 AN XY: 74336

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.626

Alfa AF: 0.587 Hom.: 8013

Bravo AF: 0.621

Asia WGS AF: 0.605 AC: 2105 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.062
DANN	Benign	0.19

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: rs2504789; hg19: chr6-39834314;