chr4-6576599-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015274.3(MAN2B2):c.160G>A(p.Ala54Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000364 in 1,613,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.160G>A | p.Ala54Thr | missense_variant | Exon 2 of 19 | 1 | NM_015274.3 | ENSP00000285599.3 | ||
MAN2B2 | ENST00000504248.5 | c.160G>A | p.Ala54Thr | missense_variant | Exon 2 of 19 | 2 | ENSP00000423129.1 | |||
MAN2B2 | ENST00000505907.1 | c.154G>A | p.Ala52Thr | missense_variant | Exon 2 of 17 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251060Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135842
GnomAD4 exome AF: 0.000363 AC: 530AN: 1460988Hom.: 0 Cov.: 31 AF XY: 0.000384 AC XY: 279AN XY: 726808
GnomAD4 genome AF: 0.000381 AC: 58AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000390 AC XY: 29AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.160G>A (p.A54T) alteration is located in exon 2 (coding exon 2) of the MAN2B2 gene. This alteration results from a G to A substitution at nucleotide position 160, causing the alanine (A) at amino acid position 54 to be replaced by a threonine (T). 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