chr3-194687715-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153690.5(FAM43A):c.889G>A(p.Glu297Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,561,462 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_153690.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM43A | NM_153690.5 | c.889G>A | p.Glu297Lys | missense_variant | 1/1 | ENST00000329759.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM43A | ENST00000329759.6 | c.889G>A | p.Glu297Lys | missense_variant | 1/1 | NM_153690.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 1932AN: 152204Hom.: 49 Cov.: 33
GnomAD3 exomes AF: 0.00280 AC: 458AN: 163812Hom.: 10 AF XY: 0.00199 AC XY: 173AN XY: 87056
GnomAD4 exome AF: 0.00118 AC: 1662AN: 1409140Hom.: 35 Cov.: 30 AF XY: 0.00103 AC XY: 717AN XY: 695842
GnomAD4 genome AF: 0.0127 AC: 1931AN: 152322Hom.: 49 Cov.: 33 AF XY: 0.0121 AC XY: 901AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at