rs1721359

chr2-227887158-G-A

Variant summary

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

The NM_178821.3(DAW1):c.113+1735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,092 control chromosomes in the GnomAD database, including 40,037 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 0.72 (40037 hom., cov: 31)
• Consequence: DAW1 NM_178821.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

DAW1 (HGNC:26383): (dynein assembly factor with WD repeats 1) Predicted to act upstream of or within several processes, including cerebrospinal fluid circulation; determination of left/right symmetry; and outer dynein arm assembly. Predicted to be located in cilium and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAW1	NM_178821.3	c.113+1735G>A		intron_variant		ENST00000309931.3
DAW1	NM_001330004.2	c.68+1735G>A		intron_variant
DAW1	XM_047443536.1	c.68+1735G>A		intron_variant
DAW1	NR_138459.2	n.172+1735G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAW1	ENST00000309931.3	c.113+1735G>A		intron_variant		1	NM_178821.3	P1
DAW1	ENST00000440997.1	c.68+1735G>A		intron_variant		4
DAW1	ENST00000373666.6	c.113+1735G>A		intron_variant, NMD_transcript_variant		2
DAW1	ENST00000454999.5	c.*54+1735G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110003 AN: 151976 Hom.: 40035 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.724 AC: 110048 AN: 152092 Hom.: 40037 Cov.: 31 AF XY: 0.720 AC XY: 53543 AN XY: 74350

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.738

Alfa AF: 0.751 Hom.: 8052

Bravo AF: 0.726

Asia WGS AF: 0.613 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.46

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

Other links and lift over

dbSNP: rs1721359; hg19: chr2-228751874;