chr20-49373713-G-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_004975.4(KCNB1):c.1847C>G(p.Thr616Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0183 in 1,614,164 control chromosomes in the GnomAD database, including 328 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T616I) has been classified as Benign.
Frequency
Consequence
NM_004975.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNB1 | NM_004975.4 | c.1847C>G | p.Thr616Ser | missense_variant | 2/2 | ENST00000371741.6 | |
LOC105372649 | XR_001754659.2 | n.1201+41689G>C | intron_variant, non_coding_transcript_variant | ||||
KCNB1 | XM_011528799.3 | c.1847C>G | p.Thr616Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNB1 | ENST00000371741.6 | c.1847C>G | p.Thr616Ser | missense_variant | 2/2 | 1 | NM_004975.4 | P1 | |
KCNB1 | ENST00000635465.1 | c.1847C>G | p.Thr616Ser | missense_variant | 3/3 | 1 | P1 | ||
ENST00000637341.1 | n.206+41689G>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
KCNB1 | ENST00000635878.1 | c.97-74330C>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0155 AC: 2361AN: 152164Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.0173 AC: 4347AN: 250860Hom.: 69 AF XY: 0.0183 AC XY: 2482AN XY: 135732
GnomAD4 exome AF: 0.0186 AC: 27151AN: 1461882Hom.: 309 Cov.: 33 AF XY: 0.0190 AC XY: 13810AN XY: 727244
GnomAD4 genome ? AF: 0.0155 AC: 2359AN: 152282Hom.: 19 Cov.: 32 AF XY: 0.0163 AC XY: 1215AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 29, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Developmental and epileptic encephalopathy, 26 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at