chr17-11816440-T-C

Position:

• chr17-11816440-T-C

Variant summary

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

The NM_001372.4(DNAH9):​c.8708-5480T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,264 control chromosomes in the GnomAD database, including 2,043 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 0.10 (2043 hom., cov: 33)
• Consequence: DNAH9 NM_001372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911

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 (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH9	NM_001372.4	c.8708-5480T>C		intron_variant		ENST00000262442.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH9	ENST00000262442.9	c.8708-5480T>C		intron_variant		1	NM_001372.4	P1
DNAH9	ENST00000454412.6	c.8708-5480T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15276 AN: 152146 Hom.: 2026 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00489

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.101 AC: 15344 AN: 152264 Hom.: 2043 Cov.: 33 AF XY: 0.0997 AC XY: 7427 AN XY: 74460

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.0715

Gnomad4 FIN AF: 0.00819

Gnomad4 NFE AF: 0.00491

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0561 Hom.: 134

Bravo AF: 0.112

Asia WGS AF: 0.138 AC: 479 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	0.67
DANN	Benign	0.50

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: rs10521191; hg19: chr17-11719757;