chr5-170383695-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004137.4(KCNMB1):c.290G>A(p.Arg97Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000398 in 1,613,988 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 (★).
Frequency
Consequence
NM_004137.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNMB1 | NM_004137.4 | c.290G>A | p.Arg97Gln | missense_variant | 3/4 | ENST00000274629.9 | |
KCNIP1 | NM_001034838.3 | c.88+29731C>T | intron_variant | ||||
KCNIP1 | XM_017009407.2 | c.88+29731C>T | intron_variant | ||||
KCNIP1 | XM_017009408.2 | c.88+29731C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNMB1 | ENST00000274629.9 | c.290G>A | p.Arg97Gln | missense_variant | 3/4 | 1 | NM_004137.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251402Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135884
GnomAD4 exome AF: 0.000420 AC: 614AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.000426 AC XY: 310AN XY: 727246
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.290G>A (p.R97Q) alteration is located in exon 3 (coding exon 2) of the KCNMB1 gene. This alteration results from a G to A substitution at nucleotide position 290, causing the arginine (R) at amino acid position 97 to be replaced by a glutamine (Q). 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