Variant chr17-78495112-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.5904-15C>T variant causes a splice polypyrimidine tract, 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 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.469

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 17-78495112-G-A is Benign according to our data. Variant chr17-78495112-G-A is described in ClinVar as [Benign]. Clinvar id 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/exons	MANE	Protein	UniProt
DNAH17	NM_173628.4 linkuse as main transcript	c.5904-15C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000389840.7	NP_775899.3
DNAH17-AS1	NR_102401.1 linkuse as main transcript	n.769+915G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.5904-15C>T		splice_polypyrimidine_tract_variant, intron_variant		5	NM_173628.4	ENSP00000374490	P1	Q9UFH2-1
DNAH17-AS1	ENST00000591373.2 linkuse as main transcript	n.769+915G>A		intron_variant, non_coding_transcript_variant		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

GnomAD3 exomes

AF:

0.276

AC:

59254

AN:

214656

Hom.:

8442

AF XY:

0.277

AC XY:

32269

AN XY:

116412

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 SAS exome

AF:

0.341

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

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.360

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.264

Gnomad4 SAS exome

AF:

0.340

Gnomad4 FIN exome

AF:

0.230

Gnomad4 NFE exome

AF:

0.259

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.230

AC:

35058

AN:

152180

Hom.:

4302

Cov.:

AF XY:

0.232

AC XY:

17236

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.257

Gnomad4 EAS

AF:

0.254

Gnomad4 SAS

AF:

0.339

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.255

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.254

Hom.:

7439

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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

DANN

Benign

0.33

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