chr2-158340277-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_138803.4(CCDC148):c.451C>A(p.His151Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_138803.4 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
CCDC148 | NM_138803.4 | c.451C>A | p.His151Asn | missense_variant | 5/14 | ENST00000283233.10 | |
CCDC148 | NM_001301685.2 | c.451C>A | p.His151Asn | missense_variant | 5/7 | ||
CCDC148 | NM_001301684.2 | c.48+321C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC148 | ENST00000283233.10 | c.451C>A | p.His151Asn | missense_variant | 5/14 | 1 | NM_138803.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251150Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135734
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461624Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 727124
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | CCDC148: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at