17-78485428-T-C

Variant names:

• chr17-78485428-T-C
• rs654154
• NM_173628.4:c.7483+122A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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-AS1 (HGNC:48594): (DNAH17 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173628.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAH17	NM_173628.4	MANE Select	c.7483+122A>G		intron	N/A	NP_775899.3	Q9UFH2-1
	DNAH17-AS1	NR_102401.1		n.253+266T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAH17	ENST00000389840.7	TSL:5 MANE Select	c.7483+122A>G		intron	N/A	ENSP00000374490.6	Q9UFH2-1
	DNAH17	ENST00000586052.5	TSL:5	n.862+122A>G		intron	N/A
	DNAH17-AS1	ENST00000588565.5	TSL:2	n.209+338T>C		intron	N/A

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

African (AFR) AF: 0.277 AC: 5471 AN: 19742

American (AMR) AF: 0.110 AC: 2823 AN: 25574

Ashkenazi Jewish (ASJ) AF: 0.0517 AC: 864 AN: 16706

East Asian (EAS) AF: 0.127 AC: 4130 AN: 32646

South Asian (SAS) AF: 0.0980 AC: 5465 AN: 55750

European-Finnish (FIN) AF: 0.0430 AC: 1408 AN: 32710

Middle Eastern (MID) AF: 0.0901 AC: 241 AN: 2674

European-Non Finnish (NFE) AF: 0.0646 AC: 36376 AN: 563230

Other (OTH) AF: 0.0877 AC: 3279 AN: 37410

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

African (AFR) AF: 0.264 AC: 10913 AN: 41410

American (AMR) AF: 0.108 AC: 1654 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3468

East Asian (EAS) AF: 0.109 AC: 562 AN: 5150

South Asian (SAS) AF: 0.105 AC: 505 AN: 4810

European-Finnish (FIN) AF: 0.0446 AC: 471 AN: 10552

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0626 AC: 4252 AN: 67924

Other (OTH) AF: 0.113 AC: 237 AN: 2106

Alfa AF: 0.0843 Hom.: 276

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.62
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs654154; hg19: chr17-76481510;