19-50320276-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004977.3(KCNC3):c.2244C>T(p.Asn748Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000029 ( 0 hom., cov: 17)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
KCNC3
NM_004977.3 synonymous
NM_004977.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.734
Genes affected
KCNC3 (HGNC:6235): (potassium voltage-gated channel subfamily C member 3) The Shaker gene family of Drosophila encodes components of voltage-gated potassium channels and is comprised of four subfamilies. Based on sequence similarity, this gene is similar to one of these subfamilies, namely the Shaw subfamily. The protein encoded by this gene belongs to the delayed rectifier class of channel proteins and is an integral membrane protein that mediates the voltage-dependent potassium ion permeability of excitable membranes. Alternate splicing results in several transcript variants. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 19-50320276-G-A is Benign according to our data. Variant chr19-50320276-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 916248.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.734 with no splicing effect.
BS2
High AC in GnomAdExome4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.2244C>T | p.Asn748Asn | synonymous_variant | 4/5 | ENST00000477616.2 | NP_004968.2 | |
KCNC3 | NM_001372305.1 | c.2016C>T | p.Asn672Asn | synonymous_variant | 4/5 | NP_001359234.1 | ||
KCNC3 | NR_110912.2 | n.260+317C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.2244C>T | p.Asn748Asn | synonymous_variant | 4/5 | 1 | NM_004977.3 | ENSP00000434241.1 | ||
KCNC3 | ENST00000670667.1 | c.2170+317C>T | intron_variant | ENSP00000499301.1 | ||||||
KCNC3 | ENST00000376959.6 | c.2170+317C>T | intron_variant | 5 | ENSP00000366158.2 | |||||
KCNC3 | ENST00000474951.1 | c.118+317C>T | intron_variant | 2 | ENSP00000432438.1 |
Frequencies
GnomAD3 genomes AF: 0.0000291 AC: 4AN: 137660Hom.: 0 Cov.: 17
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GnomAD4 exome AF: 0.0000245 AC: 23AN: 937992Hom.: 0 Cov.: 13 AF XY: 0.0000264 AC XY: 12AN XY: 453804
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GnomAD4 genome AF: 0.0000290 AC: 4AN: 137780Hom.: 0 Cov.: 17 AF XY: 0.0000300 AC XY: 2AN XY: 66720
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at