rs3743279
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001358351.3(SEMA6D):c.920A>G(p.Asn307Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0195 in 1,613,834 control chromosomes in the GnomAD database, including 2,915 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_001358351.3 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 |
---|---|---|---|---|---|---|---|
SEMA6D | NM_001358351.3 | c.920A>G | p.Asn307Ser | missense_variant | 10/19 | ENST00000536845.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6D | ENST00000536845.7 | c.920A>G | p.Asn307Ser | missense_variant | 10/19 | 2 | NM_001358351.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0735 AC: 11177AN: 152060Hom.: 1241 Cov.: 33
GnomAD3 exomes AF: 0.0343 AC: 8590AN: 250584Hom.: 728 AF XY: 0.0330 AC XY: 4466AN XY: 135408
GnomAD4 exome AF: 0.0139 AC: 20276AN: 1461656Hom.: 1665 Cov.: 33 AF XY: 0.0150 AC XY: 10935AN XY: 727136
GnomAD4 genome ? AF: 0.0738 AC: 11232AN: 152178Hom.: 1250 Cov.: 33 AF XY: 0.0725 AC XY: 5394AN XY: 74376
ClinVar
Submissions by phenotype
SEMA6D-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 14, 2020 | 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