17-78485428-T-C

Position:

• chr17-78485428-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_173628.4(DNAH17):​c.7483+122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 938,342 control chromosomes in the GnomAD database, including 4,772 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1787 hom., cov: 32)
  • Exomes 𝑓: 0.076 (2985 hom.)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.317

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-78485428-T-C is Benign according to our data. Variant chr17-78485428-T-C is described in ClinVar as [Benign]. Clinvar id is 1230694.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH17	NM_173628.4	c.7483+122A>G		intron_variant		ENST00000389840.7	NP_775899.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7	c.7483+122A>G		intron_variant		5	NM_173628.4	ENSP00000374490.6

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18806 AN: 151782 Hom.: 1780 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.115

GnomAD4 exome AF: 0.0764 AC: 60057 AN: 786442 Hom.: 2985 AF XY: 0.0763 AC XY: 30371 AN XY: 398078

Gnomad4 AFR exome AF: 0.277

Gnomad4 AMR exome AF: 0.110

Gnomad4 ASJ exome AF: 0.0517

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.0980

Gnomad4 FIN exome AF: 0.0430

Gnomad4 NFE exome AF: 0.0646

Gnomad4 OTH exome AF: 0.0877

GnomAD4 genome AF: 0.124 AC: 18848 AN: 151900 Hom.: 1787 Cov.: 32 AF XY: 0.123 AC XY: 9097 AN XY: 74240

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0453

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0626

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0866 Hom.: 168

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs654154; hg19: chr17-76481510;