4-82631385-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001037582.3(SCD5):c.935G>A(p.Arg312Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037582.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCD5 | NM_001037582.3 | c.935G>A | p.Arg312Gln | missense_variant | 5/5 | ENST00000319540.9 | NP_001032671.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCD5 | ENST00000319540.9 | c.935G>A | p.Arg312Gln | missense_variant | 5/5 | 1 | NM_001037582.3 | ENSP00000316329.4 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 76AN: 250958Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135698
GnomAD4 exome AF: 0.000427 AC: 624AN: 1461766Hom.: 0 Cov.: 31 AF XY: 0.000399 AC XY: 290AN XY: 727178
GnomAD4 genome AF: 0.000263 AC: 40AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.935G>A (p.R312Q) alteration is located in exon 5 (coding exon 5) of the SCD5 gene. This alteration results from a G to A substitution at nucleotide position 935, causing the arginine (R) at amino acid position 312 to be replaced by a glutamine (Q). 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