9-89379088-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001371194.2(SEMA4D):c.2205C>T(p.Leu735Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,614,138 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 (no stars).
Frequency
Consequence
NM_001371194.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA4D | NM_001371194.2 | c.2205C>T | p.Leu735Leu | synonymous_variant | Exon 16 of 16 | ENST00000422704.7 | NP_001358123.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250920Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135658
GnomAD4 exome AF: 0.000126 AC: 184AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 88AN XY: 727194
GnomAD4 genome AF: 0.000158 AC: 24AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74494
ClinVar
Submissions by phenotype
SEMA4D-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at