17-78425279-TTTATC-T

Position:

• chr17-78425279-TTTATC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_173628.4(DNAH17):​c.13141+62_13141+66del 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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH17	NM_173628.4	c.13141+62_13141+66del		intron_variant		ENST00000389840.7	NP_775899.3
DNAH17	XM_011525416.3	c.13153+62_13153+66del		intron_variant			XP_011523718.1
DNAH17	XM_024451013.2	c.13009+62_13009+66del		intron_variant			XP_024306781.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7	c.13141+62_13141+66del		intron_variant		5	NM_173628.4	ENSP00000374490	P1
DNAH17	ENST00000591369.5	c.*72+62_*72+66del		intron_variant, NMD_transcript_variant		5		ENSP00000466150
DNAH17	ENST00000586052.5	n.6302+62_6302+66del		intron_variant, non_coding_transcript_variant		5
DNAH17	ENST00000590227.5	n.2815+62_2815+66del		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR exome AF: 0.203

Gnomad4 AMR exome AF: 0.124

Gnomad4 ASJ exome AF: 0.244

Gnomad4 EAS exome AF: 0.0213

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.170

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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.178

Alfa AF: 0.178 Hom.: 292

Bravo AF: 0.179

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs143392722; hg19: chr17-76421360;