19-50314777-TCCCCACC-TCCCCACCCCCCACC

Variant names:

• chr19-50314777-T-TCCCCACC
• rs1022890298
• NM_004977.3:c.*1331_*1337dupGGTGGGG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_004977.3(KCNC3):​c.*1331_*1337dupGGTGGGG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000037 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNC3 NM_004977.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNC3	NM_004977.3	c.*1331_*1337dupGGTGGGG		3_prime_UTR_variant	Exon 5 of 5	ENST00000477616.2	NP_004968.2
KCNC3	NM_001372305.1	c.*1331_*1337dupGGTGGGG		3_prime_UTR_variant	Exon 5 of 5		NP_001359234.1
KCNC3	NR_110912.2	n.526_532dupGGTGGGG		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNC3	ENST00000477616	c.*1331_*1337dupGGTGGGG		3_prime_UTR_variant	Exon 5 of 5	1	NM_004977.3	ENSP00000434241.1
KCNC3	ENST00000670667	c.*70_*76dupGGTGGGG		3_prime_UTR_variant	Exon 4 of 4			ENSP00000499301.1
KCNC3	ENST00000376959	c.*249_*255dupGGTGGGG		3_prime_UTR_variant	Exon 5 of 5	5		ENSP00000366158.2
KCNC3	ENST00000474951	c.*249_*255dupGGTGGGG		3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000432438.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 151794 Hom.: 0 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000371 AC: 1 AN: 269720 Hom.: 0 Cov.: 0 AF XY: 0.00000645 AC XY: 1 AN XY: 155020

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000181

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000659 AC: 1 AN: 151794 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74156

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1022890298; hg19: chr19-50818034;