rs2504789

Variant names:

• chr6-39866538-A-G
• rs2504789
• NM_001201427.2:c.429-972A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

DAAM2-AS1 (HGNC:40830): (DAAM2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001201427.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAAM2	NM_001201427.2	MANE Select	c.429-972A>G		intron	N/A	NP_001188356.1
	DAAM2	NM_015345.4		c.429-972A>G		intron	N/A	NP_056160.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAAM2	ENST00000274867.9	TSL:1 MANE Select	c.429-972A>G		intron	N/A	ENSP00000274867.4
	DAAM2	ENST00000538976.5	TSL:1	c.429-972A>G		intron	N/A	ENSP00000437808.1
	DAAM2	ENST00000491083.2	TSL:1	n.575-972A>G		intron	N/A

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

African (AFR) AF: 0.690 AC: 28619 AN: 41492

American (AMR) AF: 0.590 AC: 9024 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2385 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2977 AN: 5178

South Asian (SAS) AF: 0.674 AC: 3248 AN: 4820

European-Finnish (FIN) AF: 0.614 AC: 6480 AN: 10562

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39187 AN: 67998

Other (OTH) AF: 0.626 AC: 1317 AN: 2104

Alfa AF: 0.588 Hom.: 10024

Bravo AF: 0.621

Asia WGS AF: 0.605 AC: 2105 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.062
DANN	Benign	0.19
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2504789; hg19: chr6-39834314;