chr7-246502-G-GGACAGGTGAGCCCTTCCTTCCTCCCTCCATCCGC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 8P and 16B. PVS1BP6_Very_StrongBA1
The NM_020223.4(FAM20C):c.953_956+30dup variant causes a stop gained, frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.283 in 1,341,114 control chromosomes in the GnomAD database, including 72,792 homozygotes. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L317L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_020223.4 stop_gained, frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM20C | NM_020223.4 | c.953_956+30dup | stop_gained, frameshift_variant | 4/10 | ENST00000313766.6 | ||
FAM20C | XR_001744837.2 | n.1503_1506+30dup | non_coding_transcript_exon_variant | 3/6 | |||
FAM20C | XR_007060116.1 | n.1582_1585+30dup | non_coding_transcript_exon_variant | 4/7 | |||
FAM20C | XR_007060117.1 | n.1503_1506+30dup | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM20C | ENST00000313766.6 | c.953_956+30dup | stop_gained, frameshift_variant | 4/10 | 1 | NM_020223.4 | P1 | ||
FAM20C | ENST00000515795.1 | n.610_613+30dup | non_coding_transcript_exon_variant | 1/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.397 AC: 43540AN: 109688Hom.: 6672 Cov.: 40
GnomAD4 exome AF: 0.273 AC: 335863AN: 1231342Hom.: 66117 Cov.: 34 AF XY: 0.274 AC XY: 167017AN XY: 610540
GnomAD4 genome ? AF: 0.397 AC: 43564AN: 109772Hom.: 6675 Cov.: 40 AF XY: 0.393 AC XY: 21057AN XY: 53590
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 13, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency - |
FAM20C-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 03, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Lethal osteosclerotic bone dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at