rs35337694

chr5-13841918-CAAAAAAAAAA-Cchr5-13841918-CAAAAAAAAAA-CAchr5-13841918-CAAAAAAAAAA-CAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAGCAATAGTAAAAAAAAAAAAAAAAAAAAAchr5-13841918-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001369.3(DNAH5):c.5272-24_5272-15del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000082 in 488,008 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000082 (0 hom.)
• Consequence: DNAH5 NM_001369.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

DNAH5 (HGNC:2950): (dynein axonemal heavy chain 5) This gene encodes a dynein protein, which is part of a microtubule-associated motor protein complex consisting of heavy, light, and intermediate chains. This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. Mutations in this gene cause primary ciliary dyskinesia type 3, as well as Kartagener syndrome, which are both diseases due to ciliary defects. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH5	NM_001369.3	c.5272-24_5272-15del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000265104.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH5	ENST00000265104.5	c.5272-24_5272-15del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001369.3	P4
DNAH5	ENST00000681290.1	c.5227-24_5227-15del		splice_polypyrimidine_tract_variant, intron_variant				A1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000820 AC: 4 AN: 488008 Hom.: 0 AF XY: 0.0000152 AC XY: 4 AN XY: 263784

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000737

Gnomad4 SAS exome AF: 0.0000222

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000316

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs35337694; hg19: chr5-13842027;