chr7-193254-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_020223.4(FAM20C):c.55G>T(p.Val19Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,466,828 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V19V) has been classified as Likely benign.
Frequency
Consequence
NM_020223.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM20C | NM_020223.4 | c.55G>T | p.Val19Leu | missense_variant | 1/10 | ENST00000313766.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM20C | ENST00000313766.6 | c.55G>T | p.Val19Leu | missense_variant | 1/10 | 1 | NM_020223.4 | P1 | |
ENST00000467050.1 | n.233+694C>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000660 AC: 99AN: 149972Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000114 AC: 13AN: 113552Hom.: 0 AF XY: 0.000112 AC XY: 7AN XY: 62326
GnomAD4 exome AF: 0.000109 AC: 144AN: 1316748Hom.: 0 Cov.: 30 AF XY: 0.000111 AC XY: 72AN XY: 650060
GnomAD4 genome ? AF: 0.000660 AC: 99AN: 150080Hom.: 0 Cov.: 33 AF XY: 0.000628 AC XY: 46AN XY: 73276
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.55G>T (p.V19L) alteration is located in exon 1 (coding exon 1) of the FAM20C gene. This alteration results from a G to T substitution at nucleotide position 55, causing the valine (V) at amino acid position 19 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at