chr7-84999443-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001384900.1(SEMA3D):c.2331G>A(p.Thr777Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,612,248 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_001384900.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA3D | NM_001384900.1 | c.2331G>A | p.Thr777Thr | synonymous_variant | Exon 19 of 19 | ENST00000284136.11 | NP_001371829.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000140 AC: 35AN: 250050Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135130
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1460004Hom.: 0 Cov.: 30 AF XY: 0.0000743 AC XY: 54AN XY: 726388
GnomAD4 genome AF: 0.000381 AC: 58AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74444
ClinVar
Submissions by phenotype
SEMA3D-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