chr17-78497489-G-A

Position:

• chr17-78497489-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173628.4(DNAH17):​c.5746-1457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 152,232 control chromosomes in the GnomAD database, including 522 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.069 (522 hom., cov: 31)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH17	NM_173628.4	c.5746-1457C>T		intron_variant		ENST00000389840.7
DNAH17-AS1	NR_102401.1	n.950+453G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH17	ENST00000389840.7	c.5746-1457C>T		intron_variant		5	NM_173628.4	P1
DNAH17-AS1	ENST00000591373.2	n.950+453G>A		intron_variant, non_coding_transcript_variant		5
DNAH17-AS1	ENST00000598378.2	n.384+453G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10501 AN: 152114 Hom.: 519 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0446

Gnomad OTH AF: 0.0573

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0691 AC: 10521 AN: 152232 Hom.: 522 Cov.: 31 AF XY: 0.0680 AC XY: 5060 AN XY: 74450

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0442

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.0298

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0446

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0556 Hom.: 59

Bravo AF: 0.0731

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs920861; hg19: chr17-76493571;