17-11799576-G-T

Variant summary

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

The NM_001372.4(DNAH9):c.8420+1783G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,340 control chromosomes in the GnomAD database, including 14,769 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 0.44 (14769 hom., cov: 30)
• Consequence: DNAH9 NM_001372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

DNAH9 (HGNC:2953): (dynein axonemal heavy chain 9) This gene encodes the heavy chain subunit of axonemal dynein, a large multi-subunit molecular motor. Axonemal dynein attaches to microtubules and hydrolyzes ATP to mediate the movement of cilia and flagella. The gene expresses at least two transcript variants; additional variants have been described, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH9	NM_001372.4	c.8420+1783G>T		intron_variant		ENST00000262442.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH9	ENST00000262442.9	c.8420+1783G>T		intron_variant		1	NM_001372.4	P1
DNAH9	ENST00000454412.6	c.8420+1783G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.436 AC: 65939 AN: 151222 Hom.: 14764 Cov.: 30

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.436 AC: 65973 AN: 151340 Hom.: 14769 Cov.: 30 AF XY: 0.433 AC XY: 32041 AN XY: 73940

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.444

Alfa AF: 0.387 Hom.: 1736

Bravo AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.51

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: rs11650055; hg19: chr17-11702893;