chr2-158340336-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_138803.4(CCDC148):c.392A>G(p.Gln131Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000618 in 1,613,986 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_138803.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC148 | NM_138803.4 | c.392A>G | p.Gln131Arg | missense_variant | 5/14 | ENST00000283233.10 | |
CCDC148 | NM_001301685.2 | c.392A>G | p.Gln131Arg | missense_variant | 5/7 | ||
CCDC148 | NM_001301684.2 | c.48+262A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC148 | ENST00000283233.10 | c.392A>G | p.Gln131Arg | missense_variant | 5/14 | 1 | NM_138803.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00313 AC: 476AN: 152218Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000832 AC: 209AN: 251312Hom.: 0 AF XY: 0.000707 AC XY: 96AN XY: 135822
GnomAD4 exome AF: 0.000356 AC: 521AN: 1461650Hom.: 2 Cov.: 31 AF XY: 0.000314 AC XY: 228AN XY: 727122
GnomAD4 genome ? AF: 0.00312 AC: 476AN: 152336Hom.: 1 Cov.: 32 AF XY: 0.00301 AC XY: 224AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at