rs146802754

Variant names:

• chr1-40820153-C-A
• rs146802754
• NM_004700.4:c.946-12C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-40820153-C-A
• chr1-40820153-C-G
• chr1-40820153-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004700.4(KCNQ4):​c.946-12C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,449,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: KCNQ4 NM_004700.4 intron
• Scores: Splicing: ADA: 0.0003396
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNQ4	NM_004700.4	c.946-12C>A		intron_variant	Intron 6 of 13	ENST00000347132.10	NP_004691.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNQ4	ENST00000347132.10	c.946-12C>A		intron_variant	Intron 6 of 13	1	NM_004700.4	ENSP00000262916.6
KCNQ4	ENST00000509682.6	c.946-12C>A		intron_variant	Intron 6 of 12	5		ENSP00000423756.2
KCNQ4	ENST00000443478.3	c.631-12C>A		intron_variant	Intron 5 of 12	5		ENSP00000406735.3
KCNQ4	ENST00000506017.1	n.265-12C>A		intron_variant	Intron 3 of 10	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1449164 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 720270

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 33090

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 43030

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25864

Gnomad4 EAS exome AF: 0.0000257 AC: 1 AN: 38934

Gnomad4 SAS exome AF: 0.0000118 AC: 1 AN: 84600

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 52590

Gnomad4 NFE exome AF: 0.00 AC: 0 AN: 1105388

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 59916

⚠️ The allele balance in gnomAD4 Exomes is highly skewed (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00034
dbscSNV1_RF	Benign	0.018
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs146802754; hg19: chr1-41285825;