chr16-1790776-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004970.3(IGFALS):c.1642C>A(p.Arg548=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000019 in 1,583,076 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.
Frequency
Consequence
NM_004970.3 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 | UniProt |
---|---|---|---|---|---|---|---|
IGFALS | NM_004970.3 | c.1642C>A | p.Arg548= | synonymous_variant | 2/2 | ENST00000215539.4 | |
IGFALS | NM_001146006.2 | c.1756C>A | p.Arg586= | synonymous_variant | 2/2 | ||
IGFALS | NR_027389.1 | n.1696C>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGFALS | ENST00000215539.4 | c.1642C>A | p.Arg548= | synonymous_variant | 2/2 | 1 | NM_004970.3 | P1 | |
IGFALS | ENST00000415638.3 | c.1756C>A | p.Arg586= | synonymous_variant | 2/2 | 2 | |||
SPSB3 | ENST00000569769.1 | c.-13+2861C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000515 AC: 1AN: 194064Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105038
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1430906Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 709400
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at