17-78425279-TTTATC-T

Variant names:

• chr17-78425279-TTTATC-T
• rs143392722
• NM_173628.4:c.13141+62_13141+66delGATAA

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+62_13141+66delGATAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,503,306 control chromosomes in the GnomAD database, including 22,990 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2366 hom., cov: 29)
  • Exomes 𝑓: 0.17 (20624 hom.)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.202
• Publications: 1 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 17-78425279-TTTATC-T is Benign according to our data. Variant chr17-78425279-TTTATC-T is described in ClinVar as Benign. ClinVar VariationId is 1242192.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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+62_13141+66delGATAA		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+62_13141+66delGATAA		intron	N/A	ENSP00000374490.6	Q9UFH2-1
	DNAH17	ENST00000586052.5	TSL:5	n.6302+62_6302+66delGATAA		intron	N/A
	DNAH17	ENST00000590227.5	TSL:2	n.2815+62_2815+66delGATAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26222 AN: 151942 Hom.: 2360 Cov.: 29

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.171 AC: 231654 AN: 1351246 Hom.: 20624 AF XY: 0.171 AC XY: 115142 AN XY: 672184

African (AFR) AF: 0.203 AC: 6227 AN: 30728

American (AMR) AF: 0.124 AC: 5026 AN: 40570

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 5621 AN: 23018

East Asian (EAS) AF: 0.0213 AC: 834 AN: 39068

South Asian (SAS) AF: 0.170 AC: 13406 AN: 78848

European-Finnish (FIN) AF: 0.118 AC: 5859 AN: 49502

Middle Eastern (MID) AF: 0.210 AC: 1141 AN: 5438

European-Non Finnish (NFE) AF: 0.179 AC: 183969 AN: 1027824

Other (OTH) AF: 0.170 AC: 9571 AN: 56250

GnomAD4 genome AF: 0.173 AC: 26251 AN: 152060 Hom.: 2366 Cov.: 29 AF XY: 0.168 AC XY: 12489 AN XY: 74330

African (AFR) AF: 0.198 AC: 8199 AN: 41478

American (AMR) AF: 0.153 AC: 2345 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3472

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5180

South Asian (SAS) AF: 0.156 AC: 754 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1214 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12090 AN: 67926

Other (OTH) AF: 0.178 AC: 375 AN: 2108

Alfa AF: 0.178 Hom.: 292

Bravo AF: 0.179

Asia WGS AF: 0.0830 AC: 288 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		-0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs143392722; hg19: chr17-76421360;