Genetic Variant DNAI2:c.-72_-63delAGCCGCGACC (chr17-74274284-GAGCCGCGACC-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_023036.6(DNAI2):c.-72_-63delAGCCGCGACC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,014 control chromosomes in the GnomAD database, including 7,254 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 7252 hom., cov: 21)

Exomes 𝑓: 0.38 ( 2 hom. )

Consequence

DNAI2
NM_023036.6 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.230

Publications

1 publications found

Variant links:

Genes affected

DNAI2 (HGNC:18744): (dynein axonemal intermediate chain 2) The protein encoded by this gene belongs to the dynein intermediate chain family, and is part of the dynein complex of respiratory cilia and sperm flagella. Mutations in this gene are associated with primary ciliary dyskinesia type 9. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]

DNAI2 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 9
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), ClinGen
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

DNAI2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 17-74274284-GAGCCGCGACC-G is Benign according to our data. Variant chr17-74274284-GAGCCGCGACC-G is described in ClinVar as [Benign]. Clinvar id is 325000.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAI2	NM_023036.6 link	c.-72_-63delAGCCGCGACC		5_prime_UTR_variant	Exon 1 of 14	ENST00000311014.11	NP_075462.3	Q9GZS0-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAI2	ENST00000311014.11 link	c.-72_-63delAGCCGCGACC	5_prime_UTR_variant	Exon 1 of 14	1	NM_023036.6	ENSP00000308312.6	Q9GZS0-1
DNAI2	ENST00000582036.5 link	c.-69_-60delAGCCGCGACC	5_prime_UTR_variant	Exon 1 of 14	1		ENSP00000461950.1	Q9GZS0-2
DNAI2	ENST00000579055.5 link	n.-72_-63delAGCCGCGACC	non_coding_transcript_exon_variant	Exon 1 of 13	2		ENSP00000462767.1	J3KT23
DNAI2	ENST00000579055.5 link	n.-72_-63delAGCCGCGACC	5_prime_UTR_variant	Exon 1 of 13	2		ENSP00000462767.1	J3KT23

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41659

AN:

151862

Hom.:

7236

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.372

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.318

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.375

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AF:

0.300

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.274

AC:

41685

AN:

151982

Hom.:

7252

Cov.:

AF XY:

0.286

AC XY:

21217

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.101

AC:

4185

AN:

41520

American (AMR)

AF:

0.414

AC:

6308

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.372

AC:

1289

AN:

3464

East Asian (EAS)

AF:

0.776

AC:

3994

AN:

5144

South Asian (SAS)

AF:

0.389

AC:

1864

AN:

4794

European-Finnish (FIN)

AF:

0.345

AC:

3647

AN:

10586

Middle Eastern (MID)

AF:

0.534

AC:

155

AN:

290

European-Non Finnish (NFE)

AF:

0.284

AC:

19310

AN:

67928

Other (OTH)

AF:

0.324

AC:

682

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

1345

2689

4034

5378

6723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.273

Hom.:

666

Bravo

AF:

0.274

Asia WGS

AF:

0.569

AC:

1975

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.23

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

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17-74274284-GAGCCGCGACC-G

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