2-162396747-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_033272.4(KCNH7):c.2606G>A(p.Ser869Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,607,904 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 Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH7 | NM_033272.4 | c.2606G>A | p.Ser869Asn | missense_variant | 11/16 | ENST00000332142.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH7 | ENST00000332142.10 | c.2606G>A | p.Ser869Asn | missense_variant | 11/16 | 1 | NM_033272.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151826Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000804 AC: 20AN: 248792Hom.: 0 AF XY: 0.0000669 AC XY: 9AN XY: 134548
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1456078Hom.: 0 Cov.: 30 AF XY: 0.00000966 AC XY: 7AN XY: 724666
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151826Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74132
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 09, 2022 | The c.2606G>A (p.S869N) alteration is located in exon 11 (coding exon 11) of the KCNH7 gene. This alteration results from a G to A substitution at nucleotide position 2606, causing the serine (S) at amino acid position 869 to be replaced by an asparagine (N). 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