Genetic Variant DNAH17:c.7483+24T>C (chr17-78485526-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_173628.4(DNAH17):c.7483+24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,551,840 control chromosomes in the GnomAD database, including 425,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 46183 hom., cov: 31)

Exomes 𝑓: 0.74 ( 379677 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.01

Publications

4 publications found

Variant links:

Genes affected

DNAH17 (HGNC:2946): (dynein axonemal heavy chain 17) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. DNAH17 is a heavy chain associated with axonemal dynein (Milisav and Affara, 1998 [PubMed 9545504]).[supplied by OMIM, Mar 2008]

DNAH17 links:

DNAH17-AS1 (HGNC:48594): (DNAH17 antisense RNA 1)

DNAH17-AS1 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=-0.91).

BP6

Variant 17-78485526-A-G is Benign according to our data. Variant chr17-78485526-A-G is described in ClinVar as Benign. ClinVar VariationId is 1269897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173628.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAH17	NM_173628.4	MANE Select	c.7483+24T>C		intron	N/A	NP_775899.3	Q9UFH2-1
	DNAH17-AS1	NR_102401.1		n.253+364A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DNAH17	ENST00000389840.7	TSL:5 MANE Select	c.7483+24T>C	intron	N/A	ENSP00000374490.6	Q9UFH2-1
DNAH17	ENST00000586052.5	TSL:5	n.862+24T>C	intron	N/A
DNAH17-AS1	ENST00000588565.5	TSL:2	n.209+436A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.777

AC:

117996

AN:

151934

Hom.:

46136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.856

Gnomad AMI

AF:

0.740

Gnomad AMR

AF:

0.833

Gnomad ASJ

AF:

0.733

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.795

Gnomad FIN

AF:

0.721

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.731

Gnomad OTH

AF:

0.786

GnomAD2 exomes

AF:

0.752

AC:

125428

AN:

166872

AF XY:

0.747

show subpopulations

Gnomad AFR exome

AF:

0.854

Gnomad AMR exome

AF:

0.861

Gnomad ASJ exome

AF:

0.713

Gnomad EAS exome

AF:

0.686

Gnomad FIN exome

AF:

0.698

Gnomad NFE exome

AF:

0.711

Gnomad OTH exome

AF:

0.751

GnomAD4 exome

AF:

0.735

AC:

1029374

AN:

1399788

Hom.:

379677

Cov.:

AF XY:

0.735

AC XY:

508307

AN XY:

691224

show subpopulations

African (AFR)

AF:

0.862

AC:

27550

AN:

31970

American (AMR)

AF:

0.856

AC:

31712

AN:

37058

Ashkenazi Jewish (ASJ)

AF:

0.718

AC:

17441

AN:

24278

East Asian (EAS)

AF:

0.696

AC:

25418

AN:

36502

South Asian (SAS)

AF:

0.797

AC:

63020

AN:

79062

European-Finnish (FIN)

AF:

0.711

AC:

33848

AN:

47622

Middle Eastern (MID)

AF:

0.754

AC:

3328

AN:

4414

European-Non Finnish (NFE)

AF:

0.725

AC:

784054

AN:

1080866

Other (OTH)

AF:

0.741

AC:

43003

AN:

58016

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

13520

27040

40561

54081

67601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19764

39528

59292

79056

98820

<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:

0.777

AC:

118105

AN:

152052

Hom.:

46183

Cov.:

AF XY:

0.777

AC XY:

57722

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.856

AC:

35531

AN:

41498

American (AMR)

AF:

0.833

AC:

12727

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.733

AC:

2541

AN:

3466

East Asian (EAS)

AF:

0.696

AC:

3584

AN:

5150

South Asian (SAS)

AF:

0.795

AC:

3838

AN:

4828

European-Finnish (FIN)

AF:

0.721

AC:

7614

AN:

10554

Middle Eastern (MID)

AF:

0.776

AC:

228

AN:

294

European-Non Finnish (NFE)

AF:

0.731

AC:

49707

AN:

67962

Other (OTH)

AF:

0.787

AC:

1662

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1356

2713

4069

5426

6782

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

862

1724

2586

3448

4310

<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:

0.753

Hom.:

7970

Bravo

AF:

0.788

Asia WGS

AF:

0.811

AC:

2822

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

(source)

DANN

Benign

0.26

PhyloP100

-1.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over