11-68903988-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002180.3(IGHMBP2):c.36G>A(p.Lys12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,400,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002180.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGHMBP2 | NM_002180.3 | c.36G>A | p.Lys12= | synonymous_variant | 1/15 | ENST00000255078.8 | |
IGHMBP2 | XM_047426881.1 | c.36G>A | p.Lys12= | synonymous_variant | 1/15 | ||
IGHMBP2 | XM_017017671.3 | c.36G>A | p.Lys12= | synonymous_variant | 1/12 | ||
IGHMBP2 | XM_005273976.3 | c.36G>A | p.Lys12= | synonymous_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGHMBP2 | ENST00000255078.8 | c.36G>A | p.Lys12= | synonymous_variant | 1/15 | 1 | NM_002180.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 35
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1400936Hom.: 0 Cov.: 44 AF XY: 0.00000145 AC XY: 1AN XY: 691482
GnomAD4 genome ? Cov.: 35
ClinVar
Submissions by phenotype
Autosomal recessive distal spinal muscular atrophy 1;C4015349:Charcot-Marie-Tooth disease axonal type 2S Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.