Variant rs78056463 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_178452.6(DNAAF1):c.352+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 1,510,580 control chromosomes in the GnomAD database, including 728 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.034 ( 142 hom., cov: 33)

Exomes 𝑓: 0.025 ( 586 hom. )

Consequence

DNAAF1
NM_178452.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.786

Variant links:

Genes affected

DNAAF1 (HGNC:30539): (dynein axonemal assembly factor 1) The protein encoded by this gene is cilium-specific and is required for the stability of the ciliary architecture. It is involved in the regulation of microtubule-based cilia and actin-based brush border microvilli. Mutations in this gene are associated with primary ciliary dyskinesia-13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

DNAAF1 links:

DNAAF1 (HGNC:):

DNAAF1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 16-84150372-G-A is Benign according to our data. Variant chr16-84150372-G-A is described in ClinVar as [Benign]. Clinvar id is 262953.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-84150372-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAAF1	NM_178452.6 linkuse as main transcript	c.352+30G>A		intron_variant		ENST00000378553.10	NP_848547.4	Q8NEP3-1A0A140VJN4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DNAAF1	ENST00000378553.10 linkuse as main transcript	c.352+30G>A	intron_variant	1	NM_178452.6	ENSP00000367815.5	Q8NEP3-1
DNAAF1	ENST00000567918.5 linkuse as main transcript	n.352+30G>A	intron_variant	1		ENSP00000455154.1	H3BP51
DNAAF1	ENST00000563093.5 linkuse as main transcript	n.352+30G>A	intron_variant	2		ENSP00000457373.1	Q8NEP3-3
DNAAF1	ENST00000570298.5 linkuse as main transcript	n.506+30G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0343

AC:

5221

AN:

152176

Hom.:

143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0672

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0263

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0394

Gnomad FIN

AF:

0.00415

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0232

Gnomad OTH

AF:

0.0320

GnomAD3 exomes

AF:

0.0263

AC:

6587

AN:

249986

Hom.:

145

AF XY:

0.0274

AC XY:

3711

AN XY:

135216

show subpopulations

Gnomad AFR exome

AF:

0.0662

Gnomad AMR exome

AF:

0.0176

Gnomad ASJ exome

AF:

0.0309

Gnomad EAS exome

AF:

0.000273

Gnomad SAS exome

AF:

0.0492

Gnomad FIN exome

AF:

0.00524

Gnomad NFE exome

AF:

0.0245

Gnomad OTH exome

AF:

0.0350

GnomAD4 exome

AF:

0.0252

AC:

34161

AN:

1358286

Hom.:

586

Cov.:

AF XY:

0.0260

AC XY:

17701

AN XY:

681858

show subpopulations

Gnomad4 AFR exome

AF:

0.0699

Gnomad4 AMR exome

AF:

0.0181

Gnomad4 ASJ exome

AF:

0.0330

Gnomad4 EAS exome

AF:

0.000153

Gnomad4 SAS exome

AF:

0.0471

Gnomad4 FIN exome

AF:

0.00589

Gnomad4 NFE exome

AF:

0.0235

Gnomad4 OTH exome

AF:

0.0299

GnomAD4 genome

AF:

0.0343

AC:

5219

AN:

152294

Hom.:

142

Cov.:

AF XY:

0.0337

AC XY:

2513

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0672

Gnomad4 AMR

AF:

0.0262

Gnomad4 ASJ

AF:

0.0346

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0384

Gnomad4 FIN

AF:

0.00415

Gnomad4 NFE

AF:

0.0232

Gnomad4 OTH

AF:

0.0312

Alfa

AF:

0.0322

Hom.:

Bravo

AF:

0.0369

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 11, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.41

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over