rs2504082

chr6-39883903-A-Gchr6-39883903-A-T

Variant summary

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

The NM_001201427.2(DAAM2):c.1846-59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 1,100,156 control chromosomes in the GnomAD database, including 102,470 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 0.44 (15273 hom., cov: 31)
  • Exomes 𝑓: 0.42 (87197 hom.)
• Consequence: DAAM2 NM_001201427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAAM2	NM_001201427.2	c.1846-59A>G		intron_variant		ENST00000274867.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAAM2	ENST00000274867.9	c.1846-59A>G		intron_variant		1	NM_001201427.2	P1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66998 AN: 151764 Hom.: 15248 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.423 AC: 401446 AN: 948270 Hom.: 87197 Cov.: 12 AF XY: 0.420 AC XY: 205378 AN XY: 489078

Gnomad4 AFR exome AF: 0.523

Gnomad4 AMR exome AF: 0.430

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.259

Gnomad4 SAS exome AF: 0.326

Gnomad4 FIN exome AF: 0.346

Gnomad4 NFE exome AF: 0.446

Gnomad4 OTH exome AF: 0.414

GnomAD4 genome AF: 0.442 AC: 67065 AN: 151886 Hom.: 15273 Cov.: 31 AF XY: 0.434 AC XY: 32191 AN XY: 74222

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.433

Alfa AF: 0.432 Hom.: 18536

Bravo AF: 0.452

Asia WGS AF: 0.287 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.3
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2504082; hg19: chr6-39851679; COSMIC: COSV51302618; COSMIC: COSV51302618;