7-21901001-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000406877.8(CDCA7L):c.*1321G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000701 in 1,425,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
CDCA7L
ENST00000406877.8 3_prime_UTR
ENST00000406877.8 3_prime_UTR
Scores
2
Splicing: ADA: 0.001619
2
Clinical Significance
Conservation
PhyloP100: 0.117
Genes affected
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]
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 7-21901001-C-T is Benign according to our data. Variant chr7-21901001-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2726490.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDCA7L | NM_018719.5 | c.*1321G>A | 3_prime_UTR_variant | 10/10 | ENST00000406877.8 | NP_061189.2 | ||
DNAH11 | NM_001277115.2 | c.13304-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000409508.8 | NP_001264044.1 | |||
CDCA7L | NM_001127370.3 | c.*1321G>A | 3_prime_UTR_variant | 11/11 | NP_001120842.1 | |||
CDCA7L | NM_001127371.3 | c.*1321G>A | 3_prime_UTR_variant | 9/9 | NP_001120843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDCA7L | ENST00000406877.8 | c.*1321G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_018719.5 | ENSP00000383986 | P1 | ||
DNAH11 | ENST00000409508.8 | c.13304-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001277115.2 | ENSP00000475939 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.01e-7 AC: 1AN: 1425678Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 706088
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33
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 25, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
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Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at