NM_001358351.3:c.302G>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001358351.3(SEMA6D):c.302G>T(p.Arg101Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,700 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 Uncertain significance (★).
Frequency
Consequence
NM_001358351.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA6D | NM_001358351.3 | c.302G>T | p.Arg101Ile | missense_variant | Exon 5 of 19 | ENST00000536845.7 | NP_001345280.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250440Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135314
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461504Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727034
GnomAD4 genome AF: 0.000131 AC: 20AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302G>T (p.R101I) alteration is located in exon 5 (coding exon 4) of the SEMA6D gene. This alteration results from a G to T substitution at nucleotide position 302, causing the arginine (R) at amino acid position 101 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at