chr2-64636589-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014755.3(SERTAD2):c.283G>A(p.Glu95Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000293 in 1,601,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014755.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERTAD2 | NM_014755.3 | c.283G>A | p.Glu95Lys | missense_variant | 2/2 | ENST00000313349.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERTAD2 | ENST00000313349.3 | c.283G>A | p.Glu95Lys | missense_variant | 2/2 | 1 | NM_014755.3 | P1 | |
SERTAD2 | ENST00000476805.2 | n.1012G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151682Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000824 AC: 2AN: 242832Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131158
GnomAD4 exome AF: 0.0000290 AC: 42AN: 1449804Hom.: 0 Cov.: 32 AF XY: 0.0000250 AC XY: 18AN XY: 719976
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151800Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74164
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2024 | The c.283G>A (p.E95K) alteration is located in exon 2 (coding exon 1) of the SERTAD2 gene. This alteration results from a G to A substitution at nucleotide position 283, causing the glutamic acid (E) at amino acid position 95 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