rs2257505
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_153706.4(SETD9):c.226T>A(p.Ser76Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 1,611,678 control chromosomes in the GnomAD database, including 419,561 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_153706.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SETD9 | NM_153706.4 | c.226T>A | p.Ser76Thr | missense_variant | 2/6 | ENST00000285947.5 | NP_714917.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SETD9 | ENST00000285947.5 | c.226T>A | p.Ser76Thr | missense_variant | 2/6 | 1 | NM_153706.4 | ENSP00000285947.2 |
Frequencies
GnomAD3 genomes AF: 0.632 AC: 96001AN: 151978Hom.: 32124 Cov.: 32
GnomAD3 exomes AF: 0.628 AC: 156517AN: 249246Hom.: 53021 AF XY: 0.639 AC XY: 86161AN XY: 134742
GnomAD4 exome AF: 0.719 AC: 1049352AN: 1459582Hom.: 387427 Cov.: 50 AF XY: 0.716 AC XY: 519475AN XY: 726024
GnomAD4 genome AF: 0.631 AC: 96046AN: 152096Hom.: 32134 Cov.: 32 AF XY: 0.624 AC XY: 46391AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at