rs17095967

Positions:

• chr14-59259085-G-A

Variant summary

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

The NM_001270520.2(DAAM1):​c.-37-4356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,082 control chromosomes in the GnomAD database, including 5,228 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 0.25 (5228 hom., cov: 32)
• Consequence: DAAM1 NM_001270520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

DAAM1 (HGNC:18142): (dishevelled associated activator of morphogenesis 1) Cell motility, adhesion, cytokinesis, and other functions of the cell cortex are mediated by reorganization of the actin cytoskeleton and several formin homology (FH) proteins have been associated with these processes. The protein encoded by this gene contains two FH domains and belongs to a novel FH protein subfamily implicated in cell polarity. A key regulator of cytoskeletal architecture, the small GTPase Rho, is activated during development by Wnt/Fz signaling to control cell polarity and movement. The protein encoded by this gene is thought to function as a scaffolding protein for the Wnt-induced assembly of a disheveled (Dvl)-Rho complex. This protein also promotes the nucleation and elongation of new actin filaments and regulates cell growth through the stabilization of microtubules. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2012]

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 (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAAM1	NM_001270520.2	c.-37-4356G>A		intron_variant		ENST00000360909.8
DAAM1	XM_005267430.3	c.-37-4356G>A		intron_variant
DAAM1	XM_005267431.2	c.-37-4356G>A		intron_variant
DAAM1	XM_047431135.1	c.-37-4356G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAAM1	ENST00000360909.8	c.-37-4356G>A		intron_variant		1	NM_001270520.2	P1
DAAM1	ENST00000556596.1	n.124-4356G>A		intron_variant, non_coding_transcript_variant		1
DAAM1	ENST00000556135.1	c.-37-4356G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38251 AN: 151964 Hom.: 5219 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.259

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.252 AC: 38294 AN: 152082 Hom.: 5228 Cov.: 32 AF XY: 0.252 AC XY: 18723 AN XY: 74334

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.261

Alfa AF: 0.250 Hom.: 2377

Bravo AF: 0.267

Asia WGS AF: 0.394 AC: 1366 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	11
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17095967; hg19: chr14-59725803;