19-50320624-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_004977.3(KCNC3):c.2139T>C(p.Tyr713=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,602 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
KCNC3
NM_004977.3 synonymous
NM_004977.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.68
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 19-50320624-A-G is Benign according to our data. Variant chr19-50320624-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1256136.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.68 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.2139T>C | p.Tyr713= | synonymous_variant | 3/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | c.1911T>C | p.Tyr637= | synonymous_variant | 3/5 | ||
KCNC3 | NR_110912.2 | n.229T>C | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.2139T>C | p.Tyr713= | synonymous_variant | 3/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000670667.1 | c.2139T>C | p.Tyr713= | synonymous_variant | 3/4 | P3 | |||
KCNC3 | ENST00000376959.6 | c.2139T>C | p.Tyr713= | synonymous_variant | 3/5 | 5 | A2 | ||
KCNC3 | ENST00000474951.1 | c.87T>C | p.Tyr29= | synonymous_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151910Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249742Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135270
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GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460692Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726640
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 01, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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