17-78485207-C-T

Position:

• chr17-78485207-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_173628.4(DNAH17):​c.7484-174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0178 in 792,166 control chromosomes in the GnomAD database, including 1,286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.060 (913 hom., cov: 31)
  • Exomes 𝑓: 0.0076 (373 hom.)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.23

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-78485207-C-T is Benign according to our data. Variant chr17-78485207-C-T is described in ClinVar as [Benign]. Clinvar id is 1269738.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH17	NM_173628.4	c.7484-174G>A		intron_variant		ENST00000389840.7	NP_775899.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7	c.7484-174G>A		intron_variant		5	NM_173628.4	ENSP00000374490.6

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9167 AN: 152054 Hom.: 909 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.00519

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000691

Gnomad OTH AF: 0.0450

GnomAD4 exome AF: 0.00760 AC: 4864 AN: 639994 Hom.: 373 Cov.: 8 AF XY: 0.00676 AC XY: 2207 AN XY: 326312

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.0147

Gnomad4 ASJ exome AF: 0.00371

Gnomad4 EAS exome AF: 0.0134

Gnomad4 SAS exome AF: 0.00558

Gnomad4 FIN exome AF: 0.0000338

Gnomad4 NFE exome AF: 0.000318

Gnomad4 OTH exome AF: 0.0145

GnomAD4 genome AF: 0.0604 AC: 9198 AN: 152172 Hom.: 913 Cov.: 31 AF XY: 0.0586 AC XY: 4360 AN XY: 74400

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0228

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.00519

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.000691

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0487 Hom.: 76

Bravo AF: 0.0703

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	-0.87
CADD	Benign	0.82
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs57434983; hg19: chr17-76481289;