rs762319130
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017950.4(CCDC40):c.1441-8G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017950.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC40 | NM_017950.4 | c.1441-8G>T | splice_region_variant, intron_variant | ENST00000397545.9 | NP_060420.2 | |||
CCDC40 | NM_001243342.2 | c.1441-8G>T | splice_region_variant, intron_variant | NP_001230271.1 | ||||
CCDC40 | NM_001330508.2 | c.1441-8G>T | splice_region_variant, intron_variant | NP_001317437.1 | ||||
LOC124904074 | XR_007065931.1 | n.305+5755C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC40 | ENST00000397545.9 | c.1441-8G>T | splice_region_variant, intron_variant | 5 | NM_017950.4 | ENSP00000380679.4 |
Frequencies
GnomAD3 genomes AF: 0.0000728 AC: 11AN: 151118Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248278Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135124
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1460768Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726710
GnomAD4 genome AF: 0.0000727 AC: 11AN: 151236Hom.: 0 Cov.: 29 AF XY: 0.000108 AC XY: 8AN XY: 73888
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 21, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at