chr12-121804754-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001353345.2(SETD1B):c.17C>A(p.Pro6His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,550,056 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P6R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001353345.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SETD1B | NM_001353345.2 | c.17C>A | p.Pro6His | missense_variant | Exon 2 of 17 | ENST00000604567.6 | NP_001340274.1 | |
SETD1B | XM_024448898.2 | c.17C>A | p.Pro6His | missense_variant | Exon 2 of 17 | XP_024304666.1 | ||
SETD1B | XM_047428552.1 | c.17C>A | p.Pro6His | missense_variant | Exon 2 of 17 | XP_047284508.1 | ||
SETD1B | XM_047428553.1 | c.17C>A | p.Pro6His | missense_variant | Exon 2 of 17 | XP_047284509.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SETD1B | ENST00000604567.6 | c.17C>A | p.Pro6His | missense_variant | Exon 2 of 17 | 5 | NM_001353345.2 | ENSP00000474253.1 | ||
SETD1B | ENST00000619791.1 | c.17C>A | p.Pro6His | missense_variant | Exon 1 of 16 | 1 | ENSP00000481531.1 | |||
SETD1B | ENST00000542440.5 | c.17C>A | p.Pro6His | missense_variant | Exon 2 of 18 | 5 | ENSP00000442924.1 |
Frequencies
GnomAD3 genomes AF: 0.000343 AC: 52AN: 151782Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000151 AC: 23AN: 152764Hom.: 0 AF XY: 0.000173 AC XY: 14AN XY: 81130
GnomAD4 exome AF: 0.0000973 AC: 136AN: 1398158Hom.: 1 Cov.: 33 AF XY: 0.0000914 AC XY: 63AN XY: 689602
GnomAD4 genome AF: 0.000349 AC: 53AN: 151898Hom.: 0 Cov.: 31 AF XY: 0.000364 AC XY: 27AN XY: 74242
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at