chr17-78425144-T-TG

Variant names:

• chr17-78425144-T-TG
• rs112942638
• NM_173628.4:c.13141+201dupC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_173628.4(DNAH17):​c.13141+201dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00631 in 581,342 control chromosomes in the GnomAD database, including 126 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (97 hom., cov: 33)
  • Exomes 𝑓: 0.0024 (29 hom.)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.36
• Publications: 0 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]

PGS1 (HGNC:30029): (phosphatidylglycerophosphate synthase 1) Predicted to enable CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity and calcium ion binding activity. Predicted to be involved in cardiolipin biosynthetic process and diacylglycerol metabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 17-78425144-T-TG is Benign according to our data. Variant chr17-78425144-T-TG is described in ClinVar as Benign. ClinVar VariationId is 1241734.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0574 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.13141+201dupC		intron	N/A	NP_775899.3	Q9UFH2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAH17	ENST00000389840.7	TSL:5 MANE Select	c.13141+201_13141+202insC		intron	N/A	ENSP00000374490.6	Q9UFH2-1
	DNAH17	ENST00000586052.5	TSL:5	n.6302+201_6302+202insC		intron	N/A
	DNAH17	ENST00000590227.5	TSL:2	n.2815+201_2815+202insC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0171 AC: 2596 AN: 152210 Hom.: 93 Cov.: 33

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00635

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000470

Gnomad OTH AF: 0.0115

GnomAD4 exome AF: 0.00241 AC: 1036 AN: 429014 Hom.: 29 Cov.: 5 AF XY: 0.00194 AC XY: 436 AN XY: 225252

African (AFR) AF: 0.0612 AC: 723 AN: 11814

American (AMR) AF: 0.00442 AC: 77 AN: 17406

Ashkenazi Jewish (ASJ) AF: 0.000155 AC: 2 AN: 12900

East Asian (EAS) AF: 0.0000344 AC: 1 AN: 29074

South Asian (SAS) AF: 0.000280 AC: 12 AN: 42860

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27054

Middle Eastern (MID) AF: 0.00421 AC: 8 AN: 1898

European-Non Finnish (NFE) AF: 0.000314 AC: 82 AN: 261300

Other (OTH) AF: 0.00530 AC: 131 AN: 24708

GnomAD4 genome AF: 0.0173 AC: 2633 AN: 152328 Hom.: 97 Cov.: 33 AF XY: 0.0169 AC XY: 1257 AN XY: 74502

African (AFR) AF: 0.0594 AC: 2469 AN: 41568

American (AMR) AF: 0.00634 AC: 97 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000470 AC: 32 AN: 68018

Other (OTH) AF: 0.0133 AC: 28 AN: 2112

Alfa AF: 0.00255 Hom.: 1

Bravo AF: 0.0196

Asia WGS AF: 0.0190 AC: 67 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
PhyloP100		-1.4
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: rs112942638; hg19: chr17-76421225;