rs756513699
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_012431.3(SEMA3E):c.870G>T(p.Ala290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A290A) has been classified as Likely benign.
Frequency
Consequence
NM_012431.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3E | NM_012431.3 | c.870G>T | p.Ala290= | synonymous_variant | 8/17 | ENST00000643230.2 | |
SEMA3E | NM_001178129.2 | c.690G>T | p.Ala230= | synonymous_variant | 8/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3E | ENST00000643230.2 | c.870G>T | p.Ala290= | synonymous_variant | 8/17 | NM_012431.3 | P1 | ||
SEMA3E | ENST00000642232.1 | c.870G>T | p.Ala290= | synonymous_variant | 8/17 | ||||
SEMA3E | ENST00000643441.1 | n.855G>T | non_coding_transcript_exon_variant | 8/17 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251034Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135670
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461244Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726934
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
CHARGE association Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at