chr8-36833658-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001031836.3(KCNU1):c.1211C>T(p.Ala404Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000316 in 1,586,416 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031836.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
KCNU1 | NM_001031836.3 | c.1211C>T | p.Ala404Val | missense_variant, splice_region_variant | 11/27 | ENST00000399881.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNU1 | ENST00000399881.8 | c.1211C>T | p.Ala404Val | missense_variant, splice_region_variant | 11/27 | 2 | NM_001031836.3 | P1 | |
KCNU1 | ENST00000522372.5 | c.1211C>T | p.Ala404Val | missense_variant, splice_region_variant, NMD_transcript_variant | 11/28 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000495 AC: 123AN: 248604Hom.: 0 AF XY: 0.000593 AC XY: 80AN XY: 134838
GnomAD4 exome AF: 0.000310 AC: 445AN: 1434266Hom.: 1 Cov.: 25 AF XY: 0.000354 AC XY: 253AN XY: 715286
GnomAD4 genome AF: 0.000375 AC: 57AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | The c.1211C>T (p.A404V) alteration is located in exon 11 (coding exon 11) of the KCNU1 gene. This alteration results from a C to T substitution at nucleotide position 1211, causing the alanine (A) at amino acid position 404 to be replaced by a valine (V). 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