dbSNP rs11077375: DNAH17:c.5904-15C>T (chr17-78495112-G-A) – 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.5904-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,585,328 control chromosomes in the GnomAD database, including 55,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4302 hom., cov: 34)

Exomes 𝑓: 0.26 ( 50734 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.469

Publications

5 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=-0.83).

BP6

Variant 17-78495112-G-A is Benign according to our data. Variant chr17-78495112-G-A is described in ClinVar as Benign. ClinVar VariationId is 402684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH17	NM_173628.4 link	c.5904-15C>T		intron_variant	Intron 38 of 80	ENST00000389840.7	NP_775899.3	Q9UFH2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 link	c.5904-15C>T		intron_variant	Intron 38 of 80	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1
DNAH17-AS1	ENST00000591373.2 link	n.769+915G>A		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

35045

AN:

152062

Hom.:

4296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.253

GnomAD2 exomes

AF:

0.276

AC:

59254

AN:

214656

AF XY:

0.277

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.371

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.256

Gnomad FIN exome

AF:

0.229

Gnomad NFE exome

AF:

0.259

Gnomad OTH exome

AF:

0.259

GnomAD4 exome

AF:

0.263

AC:

376669

AN:

1433148

Hom.:

50734

Cov.:

AF XY:

0.265

AC XY:

188326

AN XY:

709688

show subpopulations

African (AFR)

AF:

0.146

AC:

4822

AN:

33064

American (AMR)

AF:

0.360

AC:

15188

AN:

42140

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

6290

AN:

25182

East Asian (EAS)

AF:

0.264

AC:

10280

AN:

38902

South Asian (SAS)

AF:

0.340

AC:

28059

AN:

82590

European-Finnish (FIN)

AF:

0.230

AC:

11721

AN:

50978

Middle Eastern (MID)

AF:

0.260

AC:

1318

AN:

5078

European-Non Finnish (NFE)

AF:

0.259

AC:

283889

AN:

1096098

Other (OTH)

AF:

0.255

AC:

15102

AN:

59116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

13163

26326

39489

52652

65815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9754

19508

29262

39016

48770

<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:

0.230

AC:

35058

AN:

152180

Hom.:

4302

Cov.:

AF XY:

0.232

AC XY:

17236

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.154

AC:

6387

AN:

41532

American (AMR)

AF:

0.281

AC:

4308

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

891

AN:

3472

East Asian (EAS)

AF:

0.254

AC:

1312

AN:

5174

South Asian (SAS)

AF:

0.339

AC:

1637

AN:

4826

European-Finnish (FIN)

AF:

0.223

AC:

2366

AN:

10600

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.255

AC:

17339

AN:

67960

Other (OTH)

AF:

0.256

AC:

540

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1369

2738

4107

5476

6845

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<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:

0.253

Hom.:

11787

Bravo

AF:

0.232

Asia WGS

AF:

0.290

AC:

1009

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 11, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.17

(source)

DANN

Benign

0.33

PhyloP100

0.47

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