dbSNP rs11077379: DNAH17:c.2860-13C>T (chr17-78532749-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.2860-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,575,886 control chromosomes in the GnomAD database, including 216,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 20438 hom., cov: 31)

Exomes 𝑓: 0.52 ( 196124 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.320

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:

RN7SL454P (HGNC:46470): (RNA, 7SL, cytoplasmic 454, pseudogene)

RN7SL454P 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 17-78532749-G-A is Benign according to our data. Variant chr17-78532749-G-A is described in ClinVar as [Benign]. Clinvar id is 402698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH17	NM_173628.4 link	c.2860-13C>T		intron_variant	Intron 19 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.2860-13C>T		intron_variant	Intron 19 of 80	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1
RN7SL454P	ENST00000492744.3 link	n.*64C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78317

AN:

151756

Hom.:

20429

Cov.:

show subpopulations

Gnomad AFR

AF:

0.491

Gnomad AMI

AF:

0.754

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.522

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.529

Gnomad NFE

AF:

0.543

Gnomad OTH

AF:

0.525

GnomAD3 exomes

AF:

0.496

AC:

101048

AN:

203670

Hom.:

25016

AF XY:

0.500

AC XY:

54743

AN XY:

109470

show subpopulations

Gnomad AFR exome

AF:

0.474

Gnomad AMR exome

AF:

0.388

Gnomad ASJ exome

AF:

0.539

Gnomad EAS exome

AF:

0.485

Gnomad SAS exome

AF:

0.444

Gnomad FIN exome

AF:

0.560

Gnomad NFE exome

AF:

0.532

Gnomad OTH exome

AF:

0.522

GnomAD4 exome

AF:

0.524

AC:

746354

AN:

1424012

Hom.:

196124

Cov.:

AF XY:

0.523

AC XY:

368405

AN XY:

704716

show subpopulations

Gnomad4 AFR exome

AF:

0.485

Gnomad4 AMR exome

AF:

0.393

Gnomad4 ASJ exome

AF:

0.537

Gnomad4 EAS exome

AF:

0.497

Gnomad4 SAS exome

AF:

0.450

Gnomad4 FIN exome

AF:

0.565

Gnomad4 NFE exome

AF:

0.534

Gnomad4 OTH exome

AF:

0.525

GnomAD4 genome

AF:

0.516

AC:

78359

AN:

151874

Hom.:

20438

Cov.:

AF XY:

0.514

AC XY:

38154

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.491

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.522

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.517

Hom.:

2882

Bravo

AF:

0.505

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 04, 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

0.27

DANN

Benign

0.74

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