rs2504106

Variant names:

• chr6-39854343-A-G
• rs2504106
• NM_001201427.2:c.-56-1904A>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.-56-1904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,030 control chromosomes in the GnomAD database, including 28,526 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 0.61 (28526 hom., cov: 32)
• Consequence: DAAM2 NM_001201427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 6 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAAM2	NM_001201427.2	c.-56-1904A>G		intron_variant	Intron 1 of 24	ENST00000274867.9	NP_001188356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAAM2	ENST00000274867.9	c.-56-1904A>G		intron_variant	Intron 1 of 24	1	NM_001201427.2	ENSP00000274867.4

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93007 AN: 151912 Hom.: 28504 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.612 AC: 93068 AN: 152030 Hom.: 28526 Cov.: 32 AF XY: 0.613 AC XY: 45554 AN XY: 74308

African (AFR) AF: 0.650 AC: 26940 AN: 41446

American (AMR) AF: 0.599 AC: 9149 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2341 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2917 AN: 5150

South Asian (SAS) AF: 0.679 AC: 3275 AN: 4820

European-Finnish (FIN) AF: 0.615 AC: 6497 AN: 10572

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39745 AN: 67974

Other (OTH) AF: 0.628 AC: 1328 AN: 2114

Alfa AF: 0.584 Hom.: 3381

Bravo AF: 0.613

Asia WGS AF: 0.605 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.0
DANN	Benign	0.80
PhyloP100		0.64
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: rs2504106; hg19: chr6-39822119;