2-74673533-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004263.5(SEMA4F):c.627C>T(p.Ala209Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000463 in 1,614,104 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
Genomes: 𝑓 0.00048 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00046 ( 0 hom. )
Consequence
SEMA4F
NM_004263.5 synonymous
NM_004263.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.64
Genes affected
SEMA4F (HGNC:10734): (ssemaphorin 4F) This gene encodes a transmembrane class IV semaphorin family protein, which plays a role in neural development. This gene may be involved in neurogenesis in prostate cancer, the development of neurofibromas, and breast cancer tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 2-74673533-C-T is Benign according to our data. Variant chr2-74673533-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651080.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.64 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA4F | NM_004263.5 | c.627C>T | p.Ala209Ala | synonymous_variant | 6/14 | ENST00000357877.7 | NP_004254.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA4F | ENST00000357877.7 | c.627C>T | p.Ala209Ala | synonymous_variant | 6/14 | 1 | NM_004263.5 | ENSP00000350547.2 |
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152100Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000497 AC: 125AN: 251450Hom.: 0 AF XY: 0.000456 AC XY: 62AN XY: 135896
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GnomAD4 exome AF: 0.000462 AC: 675AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.000463 AC XY: 337AN XY: 727244
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GnomAD4 genome AF: 0.000480 AC: 73AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74420
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | SEMA4F: BP4, BP7 - |
Computational scores
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Benign
CADD
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