rs2322047

chr17-11712470-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.5553-6864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 151,902 control chromosomes in the GnomAD database, including 55,993 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 0.83 (55993 hom., cov: 30)
• Consequence: DNAH9 NM_001372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH9	NM_001372.4	c.5553-6864A>G		intron_variant		ENST00000262442.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH9	ENST00000262442.9	c.5553-6864A>G		intron_variant		1	NM_001372.4	P1
DNAH9	ENST00000454412.6	c.5553-6864A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126075 AN: 151784 Hom.: 55982 Cov.: 30

Gnomad AFR AF: 0.480

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.830 AC: 126112 AN: 151902 Hom.: 55993 Cov.: 30 AF XY: 0.834 AC XY: 61876 AN XY: 74232

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.871

Alfa AF: 0.928 Hom.: 23678

Bravo AF: 0.808

Asia WGS AF: 0.819 AC: 2851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.9
Dann	Benign	0.75

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: rs2322047; hg19: chr17-11615787;