16-75414582-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006324.3(CFDP1):c.178G>A(p.Ala60Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 1,603,784 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006324.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFDP1 | NM_006324.3 | c.178G>A | p.Ala60Thr | missense_variant | 2/7 | ENST00000283882.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFDP1 | ENST00000283882.4 | c.178G>A | p.Ala60Thr | missense_variant | 2/7 | 1 | NM_006324.3 | P1 | |
CFDP1 | ENST00000566901.5 | n.287G>A | non_coding_transcript_exon_variant | 2/5 | 1 | ||||
CFDP1 | ENST00000564286.1 | n.296G>A | non_coding_transcript_exon_variant | 2/5 | 5 | ||||
CFDP1 | ENST00000565646.5 | n.186-1828G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00370 AC: 563AN: 152138Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00335 AC: 841AN: 251360Hom.: 3 AF XY: 0.00330 AC XY: 448AN XY: 135858
GnomAD4 exome AF: 0.00372 AC: 5403AN: 1451528Hom.: 22 Cov.: 29 AF XY: 0.00371 AC XY: 2683AN XY: 722954
GnomAD4 genome AF: 0.00370 AC: 564AN: 152256Hom.: 1 Cov.: 32 AF XY: 0.00379 AC XY: 282AN XY: 74446
ClinVar
Submissions by phenotype
CFDP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at