9-89363482-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000420101.6(SEMA4D):c.293G>A(p.Arg98Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,613,984 control chromosomes in the GnomAD database, including 20,257 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000420101.6 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_001142287.2 | c.2138G>A | p.Arg713Lys | missense_variant | 20/21 | ||
SEMA4D | NM_001371198.1 | c.2138G>A | p.Arg713Lys | missense_variant | 18/19 | ||
SEMA4D | NM_001371199.1 | c.2138G>A | p.Arg713Lys | missense_variant | 19/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA4D | ENST00000420101.6 | c.293G>A | p.Arg98Lys | missense_variant | 2/3 | 1 | |||
SEMA4D | ENST00000475255.5 | n.2173G>A | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
SEMA4D | ENST00000339861.8 | c.2138G>A | p.Arg713Lys | missense_variant | 18/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.127 AC: 19385AN: 152144Hom.: 1801 Cov.: 33
GnomAD3 exomes AF: 0.178 AC: 44590AN: 251200Hom.: 6020 AF XY: 0.167 AC XY: 22654AN XY: 135782
GnomAD4 exome AF: 0.145 AC: 212484AN: 1461722Hom.: 18448 Cov.: 33 AF XY: 0.143 AC XY: 104305AN XY: 727170
GnomAD4 genome ? AF: 0.127 AC: 19410AN: 152262Hom.: 1809 Cov.: 33 AF XY: 0.131 AC XY: 9771AN XY: 74448
ClinVar
Submissions by phenotype
SEMA4D-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 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