rs765494674
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001112741.2(KCNC1):c.831G>A(p.Ser277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,461,878 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S277S) has been classified as Likely benign.
Frequency
Consequence
NM_001112741.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC1 | NM_001112741.2 | c.831G>A | p.Ser277= | synonymous_variant | 2/4 | ENST00000265969.8 | |
KCNC1 | NM_004976.4 | c.831G>A | p.Ser277= | synonymous_variant | 2/2 | ||
KCNC1 | XM_047426916.1 | c.831G>A | p.Ser277= | synonymous_variant | 2/4 | ||
KCNC1 | XR_930866.3 | n.2053G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC1 | ENST00000265969.8 | c.831G>A | p.Ser277= | synonymous_variant | 2/4 | 5 | NM_001112741.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251474Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135914
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727240
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Progressive myoclonic epilepsy type 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 23, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at