dbSNP rs9894913: DNAH17:c.4584+13C>T (chr17-78507445-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_173628.4(DNAH17):c.4584+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 1,612,768 control chromosomes in the GnomAD database, including 74,223 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7721 hom., cov: 33)

Exomes 𝑓: 0.30 ( 66502 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.868

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 17-78507445-G-A is Benign according to our data. Variant chr17-78507445-G-A is described in ClinVar as [Benign]. Clinvar id is 402688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH17	NM_173628.4 link	c.4584+13C>T		intron_variant	Intron 28 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.4584+13C>T		intron_variant	Intron 28 of 80	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1
DNAH17	ENST00000587177.1 link	n.636+13C>T		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47227

AN:

152020

Hom.:

7720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.0815

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.303

GnomAD3 exomes

AF:

0.277

AC:

68968

AN:

248816

Hom.:

10489

AF XY:

0.284

AC XY:

38341

AN XY:

134986

show subpopulations

Gnomad AFR exome

AF:

0.388

Gnomad AMR exome

AF:

0.187

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.0732

Gnomad SAS exome

AF:

0.365

Gnomad FIN exome

AF:

0.253

Gnomad NFE exome

AF:

0.298

Gnomad OTH exome

AF:

0.276

GnomAD4 exome

AF:

0.297

AC:

434185

AN:

1460630

Hom.:

66502

Cov.:

AF XY:

0.299

AC XY:

217479

AN XY:

726376

show subpopulations

Gnomad4 AFR exome

AF:

0.383

Gnomad4 AMR exome

AF:

0.192

Gnomad4 ASJ exome

AF:

0.327

Gnomad4 EAS exome

AF:

0.0803

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.258

Gnomad4 NFE exome

AF:

0.302

Gnomad4 OTH exome

AF:

0.300

GnomAD4 genome

AF:

0.311

AC:

47245

AN:

152138

Hom.:

7721

Cov.:

AF XY:

0.307

AC XY:

22805

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.238

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.0811

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.303

Hom.:

9979

Bravo

AF:

0.309

Asia WGS

AF:

0.238

AC:

827

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

0.29

DANN

Benign

0.44

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