16-74716507-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_024306.5(FA2H):āc.879C>Gā(p.Pro293Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,628 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P293P) has been classified as Benign.
Frequency
Consequence
NM_024306.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FA2H | NM_024306.5 | c.879C>G | p.Pro293Pro | synonymous_variant | 6/7 | ENST00000219368.8 | NP_077282.3 | |
FA2H | XM_011523319.3 | c.639C>G | p.Pro213Pro | synonymous_variant | 6/7 | XP_011521621.1 | ||
FA2H | XM_011523317.4 | c.*1743C>G | 3_prime_UTR_variant | 6/6 | XP_011521619.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FA2H | ENST00000219368.8 | c.879C>G | p.Pro293Pro | synonymous_variant | 6/7 | 1 | NM_024306.5 | ENSP00000219368.3 | ||
FA2H | ENST00000562145.1 | n.600C>G | non_coding_transcript_exon_variant | 1/2 | 1 | |||||
FA2H | ENST00000567683.5 | n.*158C>G | non_coding_transcript_exon_variant | 4/5 | 2 | ENSP00000455126.1 | ||||
FA2H | ENST00000567683.5 | n.*158C>G | 3_prime_UTR_variant | 4/5 | 2 | ENSP00000455126.1 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151628Hom.: 0 Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000753 AC: 11AN: 1461304Hom.: 0 Cov.: 64 AF XY: 0.00000550 AC XY: 4AN XY: 726954
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151628Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74010
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at