chr4-82798521-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001037582.3(SCD5):c.17C>G(p.Thr6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000375 in 1,600,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCD5 | NM_001037582.3 | c.17C>G | p.Thr6Ser | missense_variant | 1/5 | ENST00000319540.9 | |
SCD5 | NM_024906.3 | c.17C>G | p.Thr6Ser | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCD5 | ENST00000319540.9 | c.17C>G | p.Thr6Ser | missense_variant | 1/5 | 1 | NM_001037582.3 | P1 | |
SCD5 | ENST00000273908.4 | c.17C>G | p.Thr6Ser | missense_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152116Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1448546Hom.: 0 Cov.: 31 AF XY: 0.00000278 AC XY: 2AN XY: 719760
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | The c.17C>G (p.T6S) alteration is located in exon 1 (coding exon 1) of the SCD5 gene. This alteration results from a C to G substitution at nucleotide position 17, causing the threonine (T) at amino acid position 6 to be replaced by a serine (S). 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