1-40784230-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_004700.4(KCNQ4):c.137G>A(p.Gly46Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000027 in 1,221,478 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
Consequence
NM_004700.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNQ4 | NM_004700.4 | c.137G>A | p.Gly46Asp | missense_variant | Exon 1 of 14 | ENST00000347132.10 | NP_004691.2 | |
KCNQ4 | NM_172163.3 | c.137G>A | p.Gly46Asp | missense_variant | Exon 1 of 13 | NP_751895.1 | ||
KCNQ4 | XM_047434057.1 | c.137G>A | p.Gly46Asp | missense_variant | Exon 1 of 13 | XP_047290013.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNQ4 | ENST00000347132.10 | c.137G>A | p.Gly46Asp | missense_variant | Exon 1 of 14 | 1 | NM_004700.4 | ENSP00000262916.6 | ||
KCNQ4 | ENST00000509682.6 | c.137G>A | p.Gly46Asp | missense_variant | Exon 1 of 13 | 5 | ENSP00000423756.2 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 4AN: 149298Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000238 AC: 1AN: 4194Hom.: 0 AF XY: 0.000334 AC XY: 1AN XY: 2990
GnomAD4 exome AF: 0.0000271 AC: 29AN: 1072078Hom.: 0 Cov.: 30 AF XY: 0.0000350 AC XY: 18AN XY: 514674
GnomAD4 genome AF: 0.0000268 AC: 4AN: 149400Hom.: 0 Cov.: 32 AF XY: 0.0000274 AC XY: 2AN XY: 72864
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.137G>A (p.G46D) alteration is located in exon 1 (coding exon 1) of the KCNQ4 gene. This alteration results from a G to A substitution at nucleotide position 137, causing the glycine (G) at amino acid position 46 to be replaced by an aspartic acid (D). 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