chr19-38403667-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_174905.4(FAM98C):c.322G>A(p.Glu108Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0324 in 1,415,012 control chromosomes in the GnomAD database, including 807 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_174905.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM98C | NM_174905.4 | c.322G>A | p.Glu108Lys | missense_variant | 3/8 | ENST00000252530.10 | |
FAM98C | NM_001351675.1 | c.322G>A | p.Glu108Lys | missense_variant | 3/6 | ||
FAM98C | XM_017026354.2 | c.322G>A | p.Glu108Lys | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM98C | ENST00000252530.10 | c.322G>A | p.Glu108Lys | missense_variant | 3/8 | 1 | NM_174905.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0343 AC: 5216AN: 152182Hom.: 113 Cov.: 32
GnomAD3 exomes AF: 0.0259 AC: 1126AN: 43402Hom.: 15 AF XY: 0.0271 AC XY: 691AN XY: 25456
GnomAD4 exome AF: 0.0322 AC: 40660AN: 1262718Hom.: 694 Cov.: 32 AF XY: 0.0325 AC XY: 20030AN XY: 615852
GnomAD4 genome AF: 0.0343 AC: 5228AN: 152294Hom.: 113 Cov.: 32 AF XY: 0.0340 AC XY: 2533AN XY: 74458
ClinVar
Submissions by phenotype
FAM98C-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at