chr2-162394472-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_033272.4(KCNH7):c.2627G>A(p.Arg876Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000251 in 1,596,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033272.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH7 | NM_033272.4 | c.2627G>A | p.Arg876Gln | missense_variant | 12/16 | ENST00000332142.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH7 | ENST00000332142.10 | c.2627G>A | p.Arg876Gln | missense_variant | 12/16 | 1 | NM_033272.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 151832Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248700Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134460
GnomAD4 exome AF: 0.0000166 AC: 24AN: 1444274Hom.: 0 Cov.: 26 AF XY: 0.00000973 AC XY: 7AN XY: 719508
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 151832Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74118
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.2627G>A (p.R876Q) alteration is located in exon 12 (coding exon 12) of the KCNH7 gene. This alteration results from a G to A substitution at nucleotide position 2627, causing the arginine (R) at amino acid position 876 to be replaced by a glutamine (Q). 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