1-110601794-ATGTGTGTGTGTGTGTGTGTGTG-ATGTGTGTGTG

Variant names:

• chr1-110601794-ATGTGTGTGTGTG-A
• rs35728918
• NM_004974.4:c.*1477_*1488delCACACACACACA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_004974.4(KCNA2):​c.*1477_*1488delCACACACACACA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 840,436 control chromosomes in the GnomAD database, including 1 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00040 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00049 (0 hom.)
• Consequence: KCNA2 NM_004974.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 0 publications found

Genes affected

KCNA2 (HGNC:6220): (potassium voltage-gated channel subfamily A member 2) Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shaker-related subfamily. This member contains six membrane-spanning domains with a shaker-type repeat in the fourth segment. It belongs to the delayed rectifier class, members of which allow nerve cells to efficiently repolarize following an action potential. The coding region of this gene is intronless, and the gene is clustered with genes KCNA3 and KCNA10 on chromosome 1. [provided by RefSeq, Jul 2008]

KCNA2 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 32

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• genetic developmental and epileptic encephalopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• undetermined early-onset epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 54 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004974.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNA2	NM_004974.4	MANE Select	c.*1477_*1488delCACACACACACA		3_prime_UTR	Exon 3 of 3	NP_004965.1	P16389-1
	KCNA2	NM_001204269.2		c.1035+224_1035+235delCACACACACACA		intron	N/A	NP_001191198.1	P16389-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNA2	ENST00000316361.10	TSL:2 MANE Select	c.*1477_*1488delCACACACACACA		3_prime_UTR	Exon 3 of 3	ENSP00000314520.4	P16389-1
	KCNA2	ENST00000369770.7	TSL:1	c.1035+224_1035+235delCACACACACACA		intron	N/A	ENSP00000358785.3	P16389-2
	KCNA2	ENST00000633222.1	TSL:5	c.*1477_*1488delCACACACACACA		3_prime_UTR	Exon 3 of 3	ENSP00000487785.1	P16389-1

Frequencies

GnomAD3 genomes AF: 0.000397 AC: 54 AN: 135928 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000149

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00782

Gnomad SAS AF: 0.000490

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000170

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000491 AC: 346 AN: 704460 Hom.: 0 AF XY: 0.000478 AC XY: 161 AN XY: 336638

African (AFR) AF: 0.000137 AC: 2 AN: 14642

American (AMR) AF: 0.000375 AC: 2 AN: 5340

Ashkenazi Jewish (ASJ) AF: 0.000324 AC: 3 AN: 9264

East Asian (EAS) AF: 0.00737 AC: 106 AN: 14382

South Asian (SAS) AF: 0.0000790 AC: 1 AN: 12664

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10274

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1894

European-Non Finnish (NFE) AF: 0.000360 AC: 219 AN: 608540

Other (OTH) AF: 0.000473 AC: 13 AN: 27460

GnomAD4 genome AF: 0.000397 AC: 54 AN: 135976 Hom.: 1 Cov.: 0 AF XY: 0.000504 AC XY: 33 AN XY: 65460

African (AFR) AF: 0.000116 AC: 4 AN: 34382

American (AMR) AF: 0.000149 AC: 2 AN: 13460

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3330

East Asian (EAS) AF: 0.00784 AC: 35 AN: 4464

South Asian (SAS) AF: 0.000491 AC: 2 AN: 4070

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.000170 AC: 11 AN: 64854

Other (OTH) AF: 0.00 AC: 0 AN: 1892

Alfa AF: 0.00 Hom.: 69

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs35728918; hg19: chr1-111144416;