9-127816025-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001114753.3(ENG):c.1770C>A(p.Pro590=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,610,608 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. P590P) has been classified as Likely benign.
Frequency
Consequence
NM_001114753.3 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 |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.1770C>A | p.Pro590= | synonymous_variant | 14/15 | ENST00000373203.9 | |
ENG | NM_000118.4 | c.1770C>A | p.Pro590= | synonymous_variant | 14/14 | ||
ENG | NM_001278138.2 | c.1224C>A | p.Pro408= | synonymous_variant | 14/15 | ||
LOC102723566 | NR_136302.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.1770C>A | p.Pro590= | synonymous_variant | 14/15 | 1 | NM_001114753.3 | P2 | |
ENG | ENST00000344849.4 | c.1770C>A | p.Pro590= | synonymous_variant | 14/14 | 1 | A2 | ||
ENG | ENST00000480266.6 | c.1224C>A | p.Pro408= | synonymous_variant | 14/15 | 2 | |||
ENST00000439298.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243256Hom.: 0 AF XY: 0.00000757 AC XY: 1AN XY: 132068
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458382Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725182
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at