rs535365178

Variant names:

• chr6-39856434-C-A
• NM_001201427.2:c.132C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-39856434-C-A
• chr6-39856434-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001201427.2(DAAM2):​c.132C>A​(p.Asn44Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000746 in 1,339,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.5e-7 (0 hom.)
• Consequence: DAAM2 NM_001201427.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13283095).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAAM2	NM_001201427.2	c.132C>A	p.Asn44Lys	missense_variant	Exon 2 of 25	ENST00000274867.9	NP_001188356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAAM2	ENST00000274867.9	c.132C>A	p.Asn44Lys	missense_variant	Exon 2 of 25	1	NM_001201427.2	ENSP00000274867.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.46e-7 AC: 1 AN: 1339990 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 658804

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.51e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Uncertain	0.99
DEOGEN2	Benign	0.028	T;T;.;T;T
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.76
FATHMM_MKL	Benign	0.059	N
LIST_S2	Uncertain	0.93	D;.;D;D;D
M_CAP	Uncertain	0.087	D
MetaRNN	Benign	0.13	T;T;T;T;T
MetaSVM	Benign	-0.61	T
MutationAssessor	Benign	0.69	.;N;N;N;.
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-1.0	.;N;N;N;N
REVEL	Benign	0.20
Sift	Benign	0.096	.;T;T;T;T
Sift4G	Benign	0.34	T;T;T;T;T
Polyphen		0.18, 0.92	.;B;.;B;P
Vest4		0.29
MutPred		0.46		Gain of ubiquitination at N44 (P = 0.009);Gain of ubiquitination at N44 (P = 0.009);Gain of ubiquitination at N44 (P = 0.009);Gain of ubiquitination at N44 (P = 0.009);Gain of ubiquitination at N44 (P = 0.009);
MVP		0.60
MPC		0.31
ClinPred		0.13	T
GERP RS		1.7
Varity_R		0.056
gMVP		0.39

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-39824210;