Variant 17-78485531-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_173628.4(DNAH17):c.7483+19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,563,298 control chromosomes in the GnomAD database, including 1,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.062 ( 973 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 881 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.127

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 (HGNC:):

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=-0.8).

BP6

Variant 17-78485531-G-A is Benign according to our data. Variant chr17-78485531-G-A is described in ClinVar as [Benign]. Clinvar id is 1182114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH17	NM_173628.4 linkuse as main transcript	c.7483+19C>T		intron_variant		ENST00000389840.7	NP_775899.3	Q9UFH2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.7483+19C>T		intron_variant		5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1

Frequencies

GnomAD3 genomes

AF:

0.0620

AC:

9429

AN:

152100

Hom.:

967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0230

Gnomad ASJ

AF:

0.00578

Gnomad EAS

AF:

0.0212

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000735

Gnomad OTH

AF:

0.0450

GnomAD3 exomes

AF:

0.0175

AC:

3124

AN:

178608

Hom.:

265

AF XY:

0.0142

AC XY:

1367

AN XY:

96408

show subpopulations

Gnomad AFR exome

AF:

0.221

Gnomad AMR exome

AF:

0.0110

Gnomad ASJ exome

AF:

0.00313

Gnomad EAS exome

AF:

0.0228

Gnomad SAS exome

AF:

0.00573

Gnomad FIN exome

AF:

0.0000620

Gnomad NFE exome

AF:

0.000611

Gnomad OTH exome

AF:

0.00834

GnomAD4 exome

AF:

0.00705

AC:

9946

AN:

1411080

Hom.:

881

Cov.:

AF XY:

0.00626

AC XY:

4368

AN XY:

697958

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.0123

Gnomad4 ASJ exome

AF:

0.00358

Gnomad4 EAS exome

AF:

0.0143

Gnomad4 SAS exome

AF:

0.00601

Gnomad4 FIN exome

AF:

0.0000414

Gnomad4 NFE exome

AF:

0.000278

Gnomad4 OTH exome

AF:

0.0150

GnomAD4 genome

AF:

0.0622

AC:

9461

AN:

152218

Hom.:

973

Cov.:

AF XY:

0.0603

AC XY:

4487

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.0229

Gnomad4 ASJ

AF:

0.00578

Gnomad4 EAS

AF:

0.0214

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.000735

Gnomad4 OTH

AF:

0.0455

Alfa

AF:

0.0343

Hom.:

Bravo

AF:

0.0722

Asia WGS

AF:

0.0340

AC:

119

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.4

DANN

Benign

0.89

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