chr16-67657612-C-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001082486.2(ACD):c.1371G>T(p.Pro457=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.044 in 1,614,150 control chromosomes in the GnomAD database, including 1,817 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P457P) has been classified as Likely benign.
Frequency
Consequence
NM_001082486.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACD | NM_001082486.2 | c.1371G>T | p.Pro457= | synonymous_variant | 12/12 | ENST00000620761.6 | |
CARMIL2 | NM_001013838.3 | downstream_gene_variant | ENST00000334583.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACD | ENST00000620761.6 | c.1371G>T | p.Pro457= | synonymous_variant | 12/12 | 1 | NM_001082486.2 | P1 | |
CARMIL2 | ENST00000334583.11 | downstream_gene_variant | 1 | NM_001013838.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0339 AC: 5166AN: 152210Hom.: 129 Cov.: 33
GnomAD3 exomes AF: 0.0345 AC: 8661AN: 251346Hom.: 217 AF XY: 0.0349 AC XY: 4740AN XY: 135858
GnomAD4 exome AF: 0.0451 AC: 65931AN: 1461822Hom.: 1688 Cov.: 35 AF XY: 0.0442 AC XY: 32120AN XY: 727212
GnomAD4 genome ? AF: 0.0339 AC: 5164AN: 152328Hom.: 129 Cov.: 33 AF XY: 0.0332 AC XY: 2470AN XY: 74480
ClinVar
Submissions by phenotype
Dyskeratosis congenita, autosomal dominant 6 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at