1-40820153-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004700.4(KCNQ4):c.946-12C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000337 in 1,601,478 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004700.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNQ4 | ENST00000347132.10 | c.946-12C>G | intron_variant | Intron 6 of 13 | 1 | NM_004700.4 | ENSP00000262916.6 | |||
KCNQ4 | ENST00000509682.6 | c.946-12C>G | intron_variant | Intron 6 of 12 | 5 | ENSP00000423756.2 | ||||
KCNQ4 | ENST00000443478.3 | c.631-12C>G | intron_variant | Intron 5 of 12 | 5 | ENSP00000406735.3 | ||||
KCNQ4 | ENST00000506017.1 | n.265-12C>G | intron_variant | Intron 3 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152198Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00149 AC: 344AN: 230246Hom.: 8 AF XY: 0.00139 AC XY: 173AN XY: 124570
GnomAD4 exome AF: 0.000313 AC: 454AN: 1449162Hom.: 6 Cov.: 31 AF XY: 0.000314 AC XY: 226AN XY: 720270
GnomAD4 genome AF: 0.000565 AC: 86AN: 152316Hom.: 1 Cov.: 33 AF XY: 0.000644 AC XY: 48AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
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See Variant Classification Assertion Criteria. -
not specified Benign:1
c.946-12C>G in intron 6 of KCNQ4: This variant is not expected to have clinical significance because it has been identified in 2.5% (112/4416) of East Asian chr omosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.o rg; dbSNP rs146802754). -
Autosomal dominant nonsyndromic hearing loss 2A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at