chr2-158309623-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_138803.4(CCDC148):c.920A>T(p.Tyr307Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00426 in 1,612,286 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC148 | NM_138803.4 | c.920A>T | p.Tyr307Phe | missense_variant | 9/14 | ENST00000283233.10 | |
CCDC148 | NM_001301684.2 | c.482A>T | p.Tyr161Phe | missense_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC148 | ENST00000283233.10 | c.920A>T | p.Tyr307Phe | missense_variant | 9/14 | 1 | NM_138803.4 |
Frequencies
GnomAD3 genomes AF: 0.00374 AC: 569AN: 152246Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00540 AC: 1351AN: 250402Hom.: 18 AF XY: 0.00539 AC XY: 729AN XY: 135356
GnomAD4 exome AF: 0.00432 AC: 6304AN: 1459922Hom.: 30 Cov.: 31 AF XY: 0.00426 AC XY: 3094AN XY: 726344
GnomAD4 genome AF: 0.00373 AC: 568AN: 152364Hom.: 2 Cov.: 33 AF XY: 0.00378 AC XY: 282AN XY: 74514
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