19-40441825-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_203344.3(SERTAD3):c.256G>A(p.Glu86Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000504 in 1,587,734 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_203344.3 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 |
---|---|---|---|---|---|---|---|---|
SERTAD3 | NM_203344.3 | c.256G>A | p.Glu86Lys | missense_variant | Exon 2 of 2 | ENST00000322354.4 | NP_976219.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERTAD3 | ENST00000322354.4 | c.256G>A | p.Glu86Lys | missense_variant | Exon 2 of 2 | 1 | NM_203344.3 | ENSP00000325414.2 | ||
SERTAD3 | ENST00000392028.8 | c.256G>A | p.Glu86Lys | missense_variant | Exon 2 of 2 | 1 | ENSP00000375882.3 | |||
SERTAD3 | ENST00000599706.1 | c.256G>A | p.Glu86Lys | missense_variant | Exon 2 of 2 | 2 | ENSP00000469245.1 | |||
SERTAD3 | ENST00000596456.1 | c.256G>A | p.Glu86Lys | missense_variant | Exon 3 of 3 | 3 | ENSP00000472999.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000886 AC: 2AN: 225814Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122118
GnomAD4 exome AF: 0.00000418 AC: 6AN: 1435476Hom.: 0 Cov.: 33 AF XY: 0.00000422 AC XY: 3AN XY: 711652
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.256G>A (p.E86K) alteration is located in exon 2 (coding exon 1) of the SERTAD3 gene. This alteration results from a G to A substitution at nucleotide position 256, causing the glutamic acid (E) at amino acid position 86 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