rs2240519

Variant names:

• chr17-11872043-C-A
• rs2240519
• NM_001372.4:c.10242+257C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-11872043-C-A
• chr17-11872043-C-G
• chr17-11872043-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001372.4(DNAH9):​c.10242+257C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: DNAH9 NM_001372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH9	NM_001372.4	c.10242+257C>A		intron_variant	Intron 52 of 68	ENST00000262442.9	NP_001363.2
DNAH9	XM_011523703.3	c.10242+257C>A		intron_variant	Intron 52 of 69		XP_011522005.1
DNAH9	XM_017024292.3	c.10125+257C>A		intron_variant	Intron 51 of 68		XP_016879781.1
DNAH9	XM_017024293.2	c.8124+257C>A		intron_variant	Intron 41 of 58		XP_016879782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH9	ENST00000262442.9	c.10242+257C>A		intron_variant	Intron 52 of 68	1	NM_001372.4	ENSP00000262442.3
DNAH9	ENST00000454412.6	c.10242+257C>A		intron_variant	Intron 52 of 67	5		ENSP00000414874.2
DNAH9	ENST00000579703.1	c.495+2790C>A		intron_variant	Intron 2 of 3	3		ENSP00000463622.2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.78

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: rs2240519; hg19: chr17-11775360;