11-65595630-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033347.2(KCNK7):c.143C>A(p.Ala48Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,451,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033347.2 missense
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 |
---|---|---|---|---|---|---|---|
KCNK7 | NM_033347.2 | c.143C>A | p.Ala48Glu | missense_variant | 1/3 | ENST00000340313.5 | |
KCNK7 | NM_005714.2 | c.143C>A | p.Ala48Glu | missense_variant | 1/2 | ||
KCNK7 | NM_033348.2 | c.143C>A | p.Ala48Glu | missense_variant | 1/4 | ||
KCNK7 | NM_033455.2 | c.143C>A | p.Ala48Glu | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK7 | ENST00000340313.5 | c.143C>A | p.Ala48Glu | missense_variant | 1/3 | 1 | NM_033347.2 | P1 | |
KCNK7 | ENST00000394216.6 | c.143C>A | p.Ala48Glu | missense_variant | 1/2 | 1 | |||
KCNK7 | ENST00000342202.8 | c.143C>A | p.Ala48Glu | missense_variant | 1/3 | 1 | |||
KCNK7 | ENST00000394217.6 | c.143C>A | p.Ala48Glu | missense_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000173 AC: 4AN: 231604Hom.: 0 AF XY: 0.00000790 AC XY: 1AN XY: 126556
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1451696Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 721082
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2023 | The c.143C>A (p.A48E) alteration is located in exon 1 (coding exon 1) of the KCNK7 gene. This alteration results from a C to A substitution at nucleotide position 143, causing the alanine (A) at amino acid position 48 to be replaced by a glutamic acid (E). 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