8-56305697-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138969.4(SDR16C5):c.736G>A(p.Glu246Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000314 in 1,592,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138969.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDR16C5 | NM_138969.4 | c.736G>A | p.Glu246Lys | missense_variant | Exon 6 of 7 | ENST00000303749.8 | NP_620419.2 | |
SDR16C5 | NM_001318049.2 | c.736G>A | p.Glu246Lys | missense_variant | Exon 6 of 8 | NP_001304978.1 | ||
SDR16C5 | NM_001318050.2 | c.604G>A | p.Glu202Lys | missense_variant | Exon 5 of 6 | NP_001304979.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDR16C5 | ENST00000303749.8 | c.736G>A | p.Glu246Lys | missense_variant | Exon 6 of 7 | 1 | NM_138969.4 | ENSP00000307607.3 | ||
SDR16C5 | ENST00000396721.6 | c.604G>A | p.Glu202Lys | missense_variant | Exon 5 of 6 | 1 | ENSP00000379947.2 | |||
SDR16C5 | ENST00000522671.1 | c.736G>A | p.Glu246Lys | missense_variant | Exon 6 of 8 | 2 | ENSP00000431010.1 |
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 4AN: 151092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000861 AC: 2AN: 232308Hom.: 0 AF XY: 0.00000795 AC XY: 1AN XY: 125814
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1441210Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 715874
GnomAD4 genome AF: 0.0000265 AC: 4AN: 151208Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73764
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.736G>A (p.E246K) alteration is located in exon 6 (coding exon 5) of the SDR16C5 gene. This alteration results from a G to A substitution at nucleotide position 736, causing the glutamic acid (E) at amino acid position 246 to be replaced by a lysine (K). 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