Variant 6-39856329-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001201427.2(DAAM2):c.27T>C(p.His9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 1,548,998 control chromosomes in the GnomAD database, including 288 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.012 ( 20 hom., cov: 32)

Exomes 𝑓: 0.014 ( 268 hom. )

Consequence

DAAM2
NM_001201427.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.61

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 6-39856329-T-C is Benign according to our data. Variant chr6-39856329-T-C is described in ClinVar as [Benign]. Clinvar id is 3060337.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=2.61 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAAM2	NM_001201427.2 linkuse as main transcript	c.27T>C	p.His9=	synonymous_variant	2/25	ENST00000274867.9	NP_001188356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAAM2	ENST00000274867.9 linkuse as main transcript	c.27T>C	p.His9=	synonymous_variant	2/25	1	NM_001201427.2	ENSP00000274867	P1	Q86T65-3

Frequencies

GnomAD3 genomes

AF:

0.0122

AC:

1859

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00536

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0147

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.0591

Gnomad SAS

AF:

0.00973

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0135

AC:

2240

AN:

165822

Hom.:

AF XY:

0.0138

AC XY:

1224

AN XY:

88824

show subpopulations

Gnomad AFR exome

AF:

0.00375

Gnomad AMR exome

AF:

0.0105

Gnomad ASJ exome

AF:

0.00854

Gnomad EAS exome

AF:

0.0569

Gnomad SAS exome

AF:

0.00683

Gnomad FIN exome

AF:

0.00454

Gnomad NFE exome

AF:

0.0139

Gnomad OTH exome

AF:

0.0136

GnomAD4 exome

AF:

0.0142

AC:

19792

AN:

1396676

Hom.:

268

Cov.:

AF XY:

0.0140

AC XY:

9690

AN XY:

690098

show subpopulations

Gnomad4 AFR exome

AF:

0.00566

Gnomad4 AMR exome

AF:

0.00989

Gnomad4 ASJ exome

AF:

0.00772

Gnomad4 EAS exome

AF:

0.0756

Gnomad4 SAS exome

AF:

0.00695

Gnomad4 FIN exome

AF:

0.00530

Gnomad4 NFE exome

AF:

0.0135

Gnomad4 OTH exome

AF:

0.0146

GnomAD4 genome

AF:

0.0122

AC:

1859

AN:

152322

Hom.:

Cov.:

AF XY:

0.0118

AC XY:

880

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00539

Gnomad4 AMR

AF:

0.0146

Gnomad4 ASJ

AF:

0.00865

Gnomad4 EAS

AF:

0.0591

Gnomad4 SAS

AF:

0.00973

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.00999

Hom.:

Bravo

AF:

0.0124

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DAAM2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 19, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

8.5

DANN

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over