9-89378700-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001371194.2(SEMA4D):c.*4C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 1,608,650 control chromosomes in the GnomAD database, including 554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.033 ( 315 hom., cov: 33)
Exomes 𝑓: 0.0035 ( 239 hom. )
Consequence
SEMA4D
NM_001371194.2 3_prime_UTR
NM_001371194.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.596
Genes affected
SEMA4D (HGNC:10732): (semaphorin 4D) Enables identical protein binding activity; semaphorin receptor binding activity; and transmembrane signaling receptor activity. Involved in several processes, including positive regulation of phosphatidylinositol 3-kinase signaling; regulation of neuron projection development; and regulation of phosphate metabolic process. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 9-89378700-G-A is Benign according to our data. Variant chr9-89378700-G-A is described in ClinVar as [Benign]. Clinvar id is 3039346.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA4D | NM_001371194.2 | c.*4C>T | 3_prime_UTR_variant | 16/16 | ENST00000422704.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA4D | ENST00000422704.7 | c.*4C>T | 3_prime_UTR_variant | 16/16 | 1 | NM_001371194.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0332 AC: 5052AN: 152178Hom.: 313 Cov.: 33
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GnomAD3 exomes AF: 0.00877 AC: 2198AN: 250752Hom.: 117 AF XY: 0.00622 AC XY: 843AN XY: 135562
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GnomAD4 exome AF: 0.00352 AC: 5122AN: 1456354Hom.: 239 Cov.: 30 AF XY: 0.00307 AC XY: 2220AN XY: 724286
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GnomAD4 genome AF: 0.0333 AC: 5072AN: 152296Hom.: 315 Cov.: 33 AF XY: 0.0316 AC XY: 2351AN XY: 74462
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SEMA4D-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 26, 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
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at