chr4-6578556-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015274.3(MAN2B2):c.391+58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,427,880 control chromosomes in the GnomAD database, including 82,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_015274.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.391+58A>G | intron_variant | Intron 3 of 18 | 1 | NM_015274.3 | ENSP00000285599.3 | |||
MAN2B2 | ENST00000504248.5 | c.391+58A>G | intron_variant | Intron 3 of 18 | 2 | ENSP00000423129.1 | ||||
MAN2B2 | ENST00000505907.1 | c.385+58A>G | intron_variant | Intron 3 of 16 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.306 AC: 46429AN: 151880Hom.: 7550 Cov.: 32
GnomAD4 exome AF: 0.340 AC: 434056AN: 1275880Hom.: 75277 AF XY: 0.340 AC XY: 216995AN XY: 638000
GnomAD4 genome AF: 0.306 AC: 46475AN: 152000Hom.: 7563 Cov.: 32 AF XY: 0.303 AC XY: 22497AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 62% of patients studied by a panel of primary immunodeficiencies. Number of patients: 59. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at