rs878854439

Variant names:

• chr7-21901172-A-ACATCTGGACCTTCAGGCTGAAGAGCGAAGAGAAGACTGCAAAATGGGTTCTGGCTGGAGTGGCTCTGCTTCTAGAAGCGTAAGGTAACACTGGCATTCCTCTAGCCTCTGCTGGAGTGCAGTGAGGATTTTCTAGCATGTTGCTGCACTGTTCC
• rs878854439
• NM_001277115.2:c.13473_*75dupCTGGACCTTCAGGCTGAAGAGCGAAGAGAAGACTGCAAAATGGGTTCTGGCTGGAGTGGCTCTGCTTCTAGAAGCGTAAGGTAACACTGGCATTCCTCTAGCCTCTGCTGGAGTGCAGTGAGGATTTTCTAGCATGTTGCTGCACTGTTCCCAT

Variant summary

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

The NM_001277115.2(DNAH11):​c.13473_*75dupCTGGACCTTCAGGCTGAAGAGCGAAGAGAAGACTGCAAAATGGGTTCTGGCTGGAGTGGCTCTGCTTCTAGAAGCGTAAGGTAACACTGGCATTCCTCTAGCCTCTGCTGGAGTGCAGTGAGGATTTTCTAGCATGTTGCTGCACTGTTCCCAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: DNAH11 NM_001277115.2 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.41

Genes affected

DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

CDCA7L (HGNC:30777): (cell division cycle associated 7 like) Acts upstream of or within positive regulation of cell population proliferation. Located in cytosol; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2	c.13473_*75dupCTGGACCTTCAGGCTGAAGAGCGAAGAGAAGACTGCAAAATGGGTTCTGGCTGGAGTGGCTCTGCTTCTAGAAGCGTAAGGTAACACTGGCATTCCTCTAGCCTCTGCTGGAGTGCAGTGAGGATTTTCTAGCATGTTGCTGCACTGTTCCCAT		3_prime_UTR_variant	Exon 82 of 82	ENST00000409508.8	NP_001264044.1
CDCA7L	NM_018719.5	c.*996_*1149dupGGAACAGTGCAGCAACATGCTAGAAAATCCTCACTGCACTCCAGCAGAGGCTAGAGGAATGCCAGTGTTACCTTACGCTTCTAGAAGCAGAGCCACTCCAGCCAGAACCCATTTTGCAGTCTTCTCTTCGCTCTTCAGCCTGAAGGTCCAGATG		3_prime_UTR_variant	Exon 10 of 10	ENST00000406877.8	NP_061189.2
CDCA7L	NM_001127370.3	c.*996_*1149dupGGAACAGTGCAGCAACATGCTAGAAAATCCTCACTGCACTCCAGCAGAGGCTAGAGGAATGCCAGTGTTACCTTACGCTTCTAGAAGCAGAGCCACTCCAGCCAGAACCCATTTTGCAGTCTTCTCTTCGCTCTTCAGCCTGAAGGTCCAGATG		3_prime_UTR_variant	Exon 11 of 11		NP_001120842.1
CDCA7L	NM_001127371.3	c.*996_*1149dupGGAACAGTGCAGCAACATGCTAGAAAATCCTCACTGCACTCCAGCAGAGGCTAGAGGAATGCCAGTGTTACCTTACGCTTCTAGAAGCAGAGCCACTCCAGCCAGAACCCATTTTGCAGTCTTCTCTTCGCTCTTCAGCCTGAAGGTCCAGATG		3_prime_UTR_variant	Exon 9 of 9		NP_001120843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8	c.13473_*75dupCTGGACCTTCAGGCTGAAGAGCGAAGAGAAGACTGCAAAATGGGTTCTGGCTGGAGTGGCTCTGCTTCTAGAAGCGTAAGGTAACACTGGCATTCCTCTAGCCTCTGCTGGAGTGCAGTGAGGATTTTCTAGCATGTTGCTGCACTGTTCCCAT		3_prime_UTR_variant	Exon 82 of 82	5	NM_001277115.2	ENSP00000475939.1
CDCA7L	ENST00000406877	c.*996_*1149dupGGAACAGTGCAGCAACATGCTAGAAAATCCTCACTGCACTCCAGCAGAGGCTAGAGGAATGCCAGTGTTACCTTACGCTTCTAGAAGCAGAGCCACTCCAGCCAGAACCCATTTTGCAGTCTTCTCTTCGCTCTTCAGCCTGAAGGTCCAGATG		3_prime_UTR_variant	Exon 10 of 10	1	NM_018719.5	ENSP00000383986.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Primary ciliary dyskinesia Uncertain:1

Mar 08, 2016

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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: rs878854439; hg19: chr7-21940790;