4-6576719-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015274.3(MAN2B2):āc.280T>Cā(p.Tyr94His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_015274.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2B2 | NM_015274.3 | c.280T>C | p.Tyr94His | missense_variant | 2/19 | ENST00000285599.8 | |
MAN2B2 | NM_001292038.2 | c.280T>C | p.Tyr94His | missense_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.280T>C | p.Tyr94His | missense_variant | 2/19 | 1 | NM_015274.3 | P1 | |
MAN2B2 | ENST00000504248.5 | c.280T>C | p.Tyr94His | missense_variant | 2/19 | 2 | |||
MAN2B2 | ENST00000505907.1 | c.277T>C | p.Tyr93His | missense_variant | 2/17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251146Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135832
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461530Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727068
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74428
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at