rs2504082

Variant names:

• chr6-39883903-A-G
• rs2504082
• NM_001201427.2:c.1846-59A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-39883903-A-G
• chr6-39883903-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 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.1846-59A>G		intron	N/A	NP_001188356.1	Q86T65-3
	DAAM2	NM_015345.4		c.1846-59A>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.1846-59A>G		intron	N/A	ENSP00000274867.4	Q86T65-3
	DAAM2	ENST00000538976.5	TSL:1	c.1846-59A>G		intron	N/A	ENSP00000437808.1	Q86T65-4
	DAAM2	ENST00000633794.1	TSL:5	c.1846-59A>G		intron	N/A	ENSP00000488831.1	A0A0J9YYF7

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

African (AFR) AF: 0.523 AC: 12429 AN: 23754

American (AMR) AF: 0.430 AC: 16847 AN: 39218

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 9311 AN: 22286

East Asian (EAS) AF: 0.259 AC: 9464 AN: 36486

South Asian (SAS) AF: 0.326 AC: 23450 AN: 71920

European-Finnish (FIN) AF: 0.346 AC: 17816 AN: 51562

Middle Eastern (MID) AF: 0.399 AC: 1863 AN: 4664

European-Non Finnish (NFE) AF: 0.446 AC: 292304 AN: 655022

Other (OTH) AF: 0.414 AC: 17962 AN: 43358

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

African (AFR) AF: 0.526 AC: 21771 AN: 41402

American (AMR) AF: 0.441 AC: 6726 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1440 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1121 AN: 5156

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4806

European-Finnish (FIN) AF: 0.319 AC: 3358 AN: 10542

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29841 AN: 67934

Other (OTH) AF: 0.433 AC: 915 AN: 2114

Alfa AF: 0.436 Hom.: 24015

Bravo AF: 0.452

Asia WGS AF: 0.287 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.52
PhyloP100		0.0080
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2504082; hg19: chr6-39851679; COSMIC: COSV51302618; COSMIC: COSV51302618;