rs1916803

chr2-227888317-T-G

Variant summary

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

The NM_178821.3(DAW1):c.114-1539T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,030 control chromosomes in the GnomAD database, including 21,709 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 0.53 (21709 hom., cov: 33)
• Consequence: DAW1 NM_178821.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAW1	NM_178821.3	c.114-1539T>G		intron_variant		ENST00000309931.3
DAW1	NM_001330004.2	c.69-1539T>G		intron_variant
DAW1	XM_047443536.1	c.69-1539T>G		intron_variant
DAW1	NR_138459.2	n.173-1539T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAW1	ENST00000309931.3	c.114-1539T>G		intron_variant		1	NM_178821.3	P1
DAW1	ENST00000440997.1	c.69-1539T>G		intron_variant		4
DAW1	ENST00000373666.6	c.114-1539T>G		intron_variant, NMD_transcript_variant		2
DAW1	ENST00000454999.5	c.*55-1539T>G		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80669 AN: 151912 Hom.: 21700 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.531 AC: 80717 AN: 152030 Hom.: 21709 Cov.: 33 AF XY: 0.526 AC XY: 39085 AN XY: 74290

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.525

Alfa AF: 0.551 Hom.: 11336

Bravo AF: 0.543

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.4
Dann	Benign	0.78

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: rs1916803; hg19: chr2-228753033; COSMIC: COSV59367021; COSMIC: COSV59367021;