17-11965045-A-G

Variant summary

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

The NM_001372.4(DNAH9):c.13233+2789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,170 control chromosomes in the GnomAD database, including 2,592 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 0.18 (2592 hom., cov: 32)
• Consequence: DNAH9 NM_001372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH9	NM_001372.4	c.13233+2789A>G		intron_variant		ENST00000262442.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH9	ENST00000262442.9	c.13233+2789A>G		intron_variant		1	NM_001372.4	P1
	ENST00000580270.1	n.348-11041T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27504 AN: 152056 Hom.: 2584 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.181 AC: 27537 AN: 152170 Hom.: 2592 Cov.: 32 AF XY: 0.181 AC XY: 13486 AN XY: 74398

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.186

Alfa AF: 0.189 Hom.: 5630

Bravo AF: 0.185

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.0
Dann	Benign	0.61

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: rs12449769; hg19: chr17-11868362;