chr3-156384945-C-T

Variant names:

• chr3-156384945-C-T
• rs3772255
• NM_172160.3:c.276-36671C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172160.3(KCNAB1):​c.276-36671C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,026 control chromosomes in the GnomAD database, including 9,218 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (9218 hom., cov: 32)
• Consequence: KCNAB1 NM_172160.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 13 publications found

Genes affected

KCNAB1 (HGNC:6228): (potassium voltage-gated channel subfamily A regulatory beta subunit 1) 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 includes distinct isoforms which are encoded by alternatively spliced transcript variants of this gene. Some of these isoforms are beta subunits, which form heteromultimeric complexes with alpha subunits and modulate the activity of the pore-forming alpha subunits. [provided by RefSeq, Apr 2015]

ENSG00000287916 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172160.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNAB1	NM_172160.3	MANE Select	c.276-36671C>T		intron	N/A	NP_751892.1
	KCNAB1	NM_003471.3		c.243-36671C>T		intron	N/A	NP_003462.2
	KCNAB1	NM_172159.3		c.222-36671C>T		intron	N/A	NP_751891.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNAB1	ENST00000490337.6	TSL:1 MANE Select	c.276-36671C>T		intron	N/A	ENSP00000419952.1
	KCNAB1	ENST00000471742.5	TSL:1	c.243-36671C>T		intron	N/A	ENSP00000418956.1
	KCNAB1	ENST00000302490.12	TSL:1	c.222-36671C>T		intron	N/A	ENSP00000305858.8

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44901 AN: 151908 Hom.: 9170 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.261

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 45006 AN: 152026 Hom.: 9218 Cov.: 32 AF XY: 0.291 AC XY: 21602 AN XY: 74324

African (AFR) AF: 0.587 AC: 24309 AN: 41420

American (AMR) AF: 0.183 AC: 2793 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3470

East Asian (EAS) AF: 0.0504 AC: 261 AN: 5180

South Asian (SAS) AF: 0.146 AC: 703 AN: 4800

European-Finnish (FIN) AF: 0.187 AC: 1974 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13358 AN: 67984

Other (OTH) AF: 0.268 AC: 565 AN: 2112

Alfa AF: 0.346 Hom.: 5061

Bravo AF: 0.308

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3772255; hg19: chr3-156102734;