7-83961527-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006080.3(SEMA3A):c.2160G>A(p.Glu720Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000083 in 1,614,106 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 (★).
Frequency
Consequence
NM_006080.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.2160G>A | p.Glu720Glu | synonymous_variant | Exon 17 of 17 | ENST00000265362.9 | NP_006071.1 | |
SEMA3A | XM_005250110.4 | c.2160G>A | p.Glu720Glu | synonymous_variant | Exon 20 of 20 | XP_005250167.1 | ||
SEMA3A | XM_047419751.1 | c.2160G>A | p.Glu720Glu | synonymous_variant | Exon 21 of 21 | XP_047275707.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA3A | ENST00000265362.9 | c.2160G>A | p.Glu720Glu | synonymous_variant | Exon 17 of 17 | 1 | NM_006080.3 | ENSP00000265362.3 | ||
SEMA3A | ENST00000436949.5 | c.2160G>A | p.Glu720Glu | synonymous_variant | Exon 18 of 18 | 5 | ENSP00000415260.1 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251280Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135794
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461826Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727216
GnomAD4 genome AF: 0.000473 AC: 72AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74464
ClinVar
Submissions by phenotype
SEMA3A-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at