NM_001378373.1:c.161G>A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001378373.1(MBL2):c.161G>A(p.Gly54Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,613,658 control chromosomes in the GnomAD database, including 16,347 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378373.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBL2 | NM_001378373.1 | c.161G>A | p.Gly54Asp | missense_variant | Exon 2 of 5 | ENST00000674931.1 | NP_001365302.1 | |
MBL2 | NM_000242.3 | c.161G>A | p.Gly54Asp | missense_variant | Exon 1 of 4 | NP_000233.1 | ||
MBL2 | NM_001378374.1 | c.161G>A | p.Gly54Asp | missense_variant | Exon 2 of 5 | NP_001365303.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBL2 | ENST00000674931.1 | c.161G>A | p.Gly54Asp | missense_variant | Exon 2 of 5 | NM_001378373.1 | ENSP00000502789.1 | |||
MBL2 | ENST00000373968.3 | c.161G>A | p.Gly54Asp | missense_variant | Exon 1 of 4 | 1 | ENSP00000363079.3 | |||
MBL2 | ENST00000675947.1 | c.161G>A | p.Gly54Asp | missense_variant | Exon 2 of 5 | ENSP00000502615.1 |
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17710AN: 152062Hom.: 1247 Cov.: 32
GnomAD3 exomes AF: 0.141 AC: 35332AN: 251074Hom.: 2772 AF XY: 0.140 AC XY: 19047AN XY: 135682
GnomAD4 exome AF: 0.141 AC: 206058AN: 1461474Hom.: 15096 Cov.: 32 AF XY: 0.141 AC XY: 102571AN XY: 727062
GnomAD4 genome AF: 0.116 AC: 17719AN: 152184Hom.: 1251 Cov.: 32 AF XY: 0.119 AC XY: 8860AN XY: 74396
ClinVar
Submissions by phenotype
Mannose-binding lectin deficiency Pathogenic:1Benign:1Other:1
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GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
not provided Uncertain:1Benign:2
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MBL2: PS3:Moderate, PS4:Supporting -
not specified Benign:1
While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.052, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at