chr6-39864335-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001201427.2(DAAM2):​c.259-98A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 892,692 control chromosomes in the GnomAD database, including 163,306 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 ( 28865 hom., cov: 32)
Exomes 𝑓: 0.60 ( 134441 hom. )

Consequence

DAAM2
NM_001201427.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.139

Publications

6 publications found
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-AS1 (HGNC:40830): (DAAM2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DAAM2NM_001201427.2 linkc.259-98A>G intron_variant Intron 3 of 24 ENST00000274867.9 NP_001188356.1 Q86T65-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DAAM2ENST00000274867.9 linkc.259-98A>G intron_variant Intron 3 of 24 1 NM_001201427.2 ENSP00000274867.4 Q86T65-3

Frequencies

GnomAD3 genomes
AF:
0.615
AC:
93410
AN:
151894
Hom.:
28841
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.661
Gnomad AMI
AF:
0.740
Gnomad AMR
AF:
0.596
Gnomad ASJ
AF:
0.688
Gnomad EAS
AF:
0.575
Gnomad SAS
AF:
0.676
Gnomad FIN
AF:
0.623
Gnomad MID
AF:
0.687
Gnomad NFE
AF:
0.582
Gnomad OTH
AF:
0.632
GnomAD4 exome
AF:
0.600
AC:
444519
AN:
740680
Hom.:
134441
AF XY:
0.603
AC XY:
230835
AN XY:
383022
show subpopulations
African (AFR)
AF:
0.666
AC:
12350
AN:
18534
American (AMR)
AF:
0.598
AC:
16657
AN:
27872
Ashkenazi Jewish (ASJ)
AF:
0.684
AC:
12192
AN:
17816
East Asian (EAS)
AF:
0.522
AC:
17131
AN:
32802
South Asian (SAS)
AF:
0.685
AC:
40694
AN:
59450
European-Finnish (FIN)
AF:
0.612
AC:
28930
AN:
47298
Middle Eastern (MID)
AF:
0.664
AC:
2130
AN:
3210
European-Non Finnish (NFE)
AF:
0.587
AC:
292261
AN:
497876
Other (OTH)
AF:
0.619
AC:
22174
AN:
35822
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
8851
17702
26554
35405
44256
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
5294
10588
15882
21176
26470
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.615
AC:
93474
AN:
152012
Hom.:
28865
Cov.:
32
AF XY:
0.616
AC XY:
45807
AN XY:
74310
show subpopulations
African (AFR)
AF:
0.661
AC:
27409
AN:
41468
American (AMR)
AF:
0.596
AC:
9109
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.688
AC:
2385
AN:
3468
East Asian (EAS)
AF:
0.574
AC:
2963
AN:
5162
South Asian (SAS)
AF:
0.674
AC:
3249
AN:
4822
European-Finnish (FIN)
AF:
0.623
AC:
6580
AN:
10560
Middle Eastern (MID)
AF:
0.701
AC:
206
AN:
294
European-Non Finnish (NFE)
AF:
0.582
AC:
39571
AN:
67940
Other (OTH)
AF:
0.630
AC:
1329
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1876
3752
5629
7505
9381
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
778
1556
2334
3112
3890
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.592
Hom.:
3842
Bravo
AF:
0.616
Asia WGS
AF:
0.602
AC:
2097
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
4.2
DANN
Benign
0.38
PhyloP100
0.14
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

Publications

Other links and lift over

dbSNP: rs2504787; hg19: chr6-39832111; COSMIC: COSV51302053; COSMIC: COSV51302053; API