17-68555742-G-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_017565.4(FAM20A):c.406C>A(p.Arg136=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_017565.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM20A | NM_017565.4 | c.406C>A | p.Arg136= | splice_region_variant, synonymous_variant | 2/11 | ENST00000592554.2 | NP_060035.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM20A | ENST00000592554.2 | c.406C>A | p.Arg136= | splice_region_variant, synonymous_variant | 2/11 | 1 | NM_017565.4 | ENSP00000468308 | P1 | |
FAM20A | ENST00000226094.9 | n.63C>A | splice_region_variant, non_coding_transcript_exon_variant | 2/11 | 1 | |||||
FAM20A | ENST00000592847.1 | n.48C>A | splice_region_variant, non_coding_transcript_exon_variant | 2/8 | 3 | |||||
FAM20A | ENST00000590074.5 | c.*179C>A | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 3/12 | 2 | ENSP00000464910 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251298Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135852
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727164
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74282
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at