chr9-34512554-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012144.4(DNAI1):c.1489+130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 896,828 control chromosomes in the GnomAD database, including 73,660 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 15819 hom., cov: 32)

Exomes 𝑓: 0.39 ( 57841 hom. )

Consequence

DNAI1
NM_012144.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.326

Publications

4 publications found

Variant links:

Genes affected

DNAI1 (HGNC:2954): (dynein axonemal intermediate chain 1) This gene encodes a member of the dynein intermediate chain family. The encoded protein is part of the dynein complex in respiratory cilia. The inner- and outer-arm dyneins, which bridge between the doublet microtubules in axonemes, are the force-generating proteins responsible for the sliding movement in axonemes. The intermediate and light chains, thought to form the base of the dynein arm, help mediate attachment and may also participate in regulating dynein activity. Mutations in this gene result in abnormal ciliary ultrastructure and function associated with primary ciliary dyskinesia and Kartagener syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

DNAI1 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

DNAI1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 9-34512554-G-A is Benign according to our data. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-34512554-G-A is described in CliVar as Benign. Clinvar id is 1177022.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAI1	NM_012144.4 link	c.1489+130G>A		intron_variant	Intron 15 of 19	ENST00000242317.9	NP_036276.1	Q9UI46-1A0A140VJI0
DNAI1	NM_001281428.2 link	c.1501+130G>A		intron_variant	Intron 15 of 19		NP_001268357.1	Q9UI46A0A087WWV9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAI1	ENST00000242317.9 link	c.1489+130G>A	intron_variant	Intron 15 of 19	1	NM_012144.4	ENSP00000242317.4	Q9UI46-1
DNAI1	ENST00000614641.4 link	c.1501+130G>A	intron_variant	Intron 15 of 19	5		ENSP00000480538.1	A0A087WWV9
DNAI1	ENST00000470169.5 link	n.424+130G>A	intron_variant	Intron 3 of 5	5		ENSP00000434296.1	H0YDT9

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67425

AN:

151862

Hom.:

15798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.585

Gnomad AMI

AF:

0.505

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.388

AC:

288916

AN:

744848

Hom.:

57841

AF XY:

0.390

AC XY:

151452

AN XY:

388360

show subpopulations

African (AFR)

AF:

0.590

AC:

11173

AN:

18942

American (AMR)

AF:

0.498

AC:

17272

AN:

34652

Ashkenazi Jewish (ASJ)

AF:

0.414

AC:

8640

AN:

20882

East Asian (EAS)

AF:

0.335

AC:

10926

AN:

32642

South Asian (SAS)

AF:

0.465

AC:

30352

AN:

65308

European-Finnish (FIN)

AF:

0.436

AC:

19501

AN:

44766

Middle Eastern (MID)

AF:

0.394

AC:

1120

AN:

2844

European-Non Finnish (NFE)

AF:

0.359

AC:

175367

AN:

488354

Other (OTH)

AF:

0.400

AC:

14565

AN:

36458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9933

19865

29798

39730

49663

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3388

6776

10164

13552

16940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.444

AC:

67492

AN:

151980

Hom.:

15819

Cov.:

AF XY:

0.447

AC XY:

33226

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.585

AC:

24221

AN:

41438

American (AMR)

AF:

0.463

AC:

7079

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.414

AC:

1437

AN:

3472

East Asian (EAS)

AF:

0.347

AC:

1791

AN:

5154

South Asian (SAS)

AF:

0.457

AC:

2200

AN:

4816

European-Finnish (FIN)

AF:

0.452

AC:

4778

AN:

10560

Middle Eastern (MID)

AF:

0.401

AC:

117

AN:

292

European-Non Finnish (NFE)

AF:

0.361

AC:

24510

AN:

67942

Other (OTH)

AF:

0.426

AC:

899

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1824

3648

5471

7295

9119

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

604

1208

1812

2416

3020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.419

Hom.:

2334

Bravo

AF:

0.446

Asia WGS

AF:

0.415

AC:

1443

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 11, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Kartagener syndrome

Benign:1

Jul 01, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.68

(source)

DANN

Benign

0.22

PhyloP100

-0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over