chr11-68903962-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002180.3(IGHMBP2):c.10G>A(p.Ala4Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000709 in 1,410,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A4A) has been classified as Likely benign.
Frequency
Consequence
NM_002180.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGHMBP2 | NM_002180.3 | c.10G>A | p.Ala4Thr | missense_variant | 1/15 | ENST00000255078.8 | |
IGHMBP2 | XM_047426881.1 | c.10G>A | p.Ala4Thr | missense_variant | 1/15 | ||
IGHMBP2 | XM_017017671.3 | c.10G>A | p.Ala4Thr | missense_variant | 1/12 | ||
IGHMBP2 | XM_005273976.3 | c.10G>A | p.Ala4Thr | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGHMBP2 | ENST00000255078.8 | c.10G>A | p.Ala4Thr | missense_variant | 1/15 | 1 | NM_002180.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 35
GnomAD4 exome AF: 7.09e-7 AC: 1AN: 1410884Hom.: 0 Cov.: 43 AF XY: 0.00000143 AC XY: 1AN XY: 697666
GnomAD4 genome Cov.: 35
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 02, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at