17-78553070-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173628.4(DNAH17):c.2179-265G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,606 control chromosomes in the GnomAD database, including 12,764 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (12764 hom., cov: 29)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH17	NM_173628.4	c.2179-265G>C		intron_variant		ENST00000389840.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH17	ENST00000389840.7	c.2179-265G>C		intron_variant		5	NM_173628.4	P1
DNAH17	ENST00000589793.1	n.1391-265G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61860 AN: 151488 Hom.: 12749 Cov.: 29

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.426

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.408 AC: 61912 AN: 151606 Hom.: 12764 Cov.: 29 AF XY: 0.404 AC XY: 29902 AN XY: 74052

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.423

Alfa AF: 0.409 Hom.: 1542

Bravo AF: 0.411

Asia WGS AF: 0.433 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.46
Dann	Benign	0.42

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: rs8080186; hg19: chr17-76549152;