chr9-89402909-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001371194.2(SEMA4D):c.214G>A(p.Ala72Thr) variant causes a missense change. The variant allele was found at a frequency of 0.045 in 1,613,980 control chromosomes in the GnomAD database, including 1,945 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001371194.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA4D | NM_001371194.2 | c.214G>A | p.Ala72Thr | missense_variant | 4/16 | ENST00000422704.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA4D | ENST00000422704.7 | c.214G>A | p.Ala72Thr | missense_variant | 4/16 | 1 | NM_001371194.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0335 AC: 5103AN: 152128Hom.: 127 Cov.: 32
GnomAD3 exomes AF: 0.0357 AC: 8970AN: 251412Hom.: 197 AF XY: 0.0359 AC XY: 4878AN XY: 135876
GnomAD4 exome AF: 0.0462 AC: 67480AN: 1461734Hom.: 1818 Cov.: 32 AF XY: 0.0453 AC XY: 32908AN XY: 727148
GnomAD4 genome AF: 0.0335 AC: 5106AN: 152246Hom.: 127 Cov.: 32 AF XY: 0.0342 AC XY: 2542AN XY: 74428
ClinVar
Submissions by phenotype
SEMA4D-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as 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