chr2-158250873-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_138803.4(CCDC148):c.1150C>T(p.Leu384=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,603,370 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00017 ( 2 hom. )
Consequence
CCDC148
NM_138803.4 synonymous
NM_138803.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.199
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 2-158250873-G-A is Benign according to our data. Variant chr2-158250873-G-A is described in ClinVar as [Benign]. Clinvar id is 795160.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.199 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC148 | NM_138803.4 | c.1150C>T | p.Leu384= | synonymous_variant | 10/14 | ENST00000283233.10 | |
CCDC148 | NM_001301684.2 | c.712C>T | p.Leu238= | synonymous_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC148 | ENST00000283233.10 | c.1150C>T | p.Leu384= | synonymous_variant | 10/14 | 1 | NM_138803.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000107 AC: 16AN: 149432Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000365 AC: 89AN: 243624Hom.: 0 AF XY: 0.000530 AC XY: 70AN XY: 132194
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GnomAD4 exome AF: 0.000167 AC: 243AN: 1453822Hom.: 2 Cov.: 31 AF XY: 0.000256 AC XY: 185AN XY: 723330
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at