rs537008263
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_004700.4(KCNQ4):c.*7T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,613,550 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
KCNQ4
NM_004700.4 3_prime_UTR
NM_004700.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.644
Genes affected
KCNQ4 (HGNC:6298): (potassium voltage-gated channel subfamily Q member 4) The protein encoded by this gene forms a potassium channel that is thought to play a critical role in the regulation of neuronal excitability, particularly in sensory cells of the cochlea. The current generated by this channel is inhibited by M1 muscarinic acetylcholine receptors and activated by retigabine, a novel anti-convulsant drug. The encoded protein can form a homomultimeric potassium channel or possibly a heteromultimeric channel in association with the protein encoded by the KCNQ3 gene. Defects in this gene are a cause of nonsyndromic sensorineural deafness type 2 (DFNA2), an autosomal dominant form of progressive hearing loss. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000328 (50/152310) while in subpopulation AFR AF= 0.0012 (50/41574). AF 95% confidence interval is 0.000937. There are 0 homozygotes in gnomad4. There are 20 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 50 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNQ4 | NM_004700.4 | c.*7T>C | 3_prime_UTR_variant | 14/14 | ENST00000347132.10 | NP_004691.2 | ||
KCNQ4 | NM_172163.3 | c.*7T>C | 3_prime_UTR_variant | 13/13 | NP_751895.1 | |||
KCNQ4 | XM_017002792.2 | c.*7T>C | 3_prime_UTR_variant | 11/11 | XP_016858281.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNQ4 | ENST00000347132.10 | c.*7T>C | 3_prime_UTR_variant | 14/14 | 1 | NM_004700.4 | ENSP00000262916.6 | |||
KCNQ4 | ENST00000443478.3 | c.*7T>C | 3_prime_UTR_variant | 13/13 | 5 | ENSP00000406735.3 | ||||
KCNQ4 | ENST00000506017.1 | n.1414T>C | non_coding_transcript_exon_variant | 11/11 | 2 | |||||
KCNQ4 | ENST00000509682.6 | c.*7T>C | downstream_gene_variant | 5 | ENSP00000423756.2 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152192Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251100Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135822
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GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461240Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 726996
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GnomAD4 genome AF: 0.000328 AC: 50AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74482
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 15, 2015 | The c.*7T>C variant in KCNQ4 has not been previously reported in individuals wit h hearing loss, but has been identified in 9/10338 African chromosomes by the Ex ome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs537008 263). Although this variant has been seen in the general population, its freque ncy is not high enough to rule out a pathogenic role. This variant occurs in the 3' untranslated region (3' UTR) and does not affect the coding sequence of the gene. Although this region can contain elements that regulate mRNA, there is no obvious predicted effect of this variant. In summary, the clinical significance of the c.*7T>C variant is uncertain. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at