chr1-111932307-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378969.1(KCND3):​c.1106+49314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,110 control chromosomes in the GnomAD database, including 45,492 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 0.76 ( 45492 hom., cov: 32)

Consequence

KCND3
NM_001378969.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.237
Variant links:
Genes affected
KCND3 (HGNC:6239): (potassium voltage-gated channel subfamily D member 3) Voltage-gated potassium (Kv) 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, shal-related subfamily, members of which form voltage-activated A-type potassium ion channels and are prominent in the repolarization phase of the action potential. This member includes two isoforms with different sizes, which are encoded by alternatively spliced transcript variants of this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCND3NM_001378969.1 linkc.1106+49314G>A intron_variant Intron 2 of 7 ENST00000302127.5 NP_001365898.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCND3ENST00000302127.5 linkc.1106+49314G>A intron_variant Intron 2 of 7 5 NM_001378969.1 ENSP00000306923.4 Q9UK17-1

Frequencies

GnomAD3 genomes
AF:
0.761
AC:
115658
AN:
151992
Hom.:
45490
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.549
Gnomad AMI
AF:
0.854
Gnomad AMR
AF:
0.742
Gnomad ASJ
AF:
0.887
Gnomad EAS
AF:
0.834
Gnomad SAS
AF:
0.766
Gnomad FIN
AF:
0.757
Gnomad MID
AF:
0.844
Gnomad NFE
AF:
0.880
Gnomad OTH
AF:
0.801
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.761
AC:
115695
AN:
152110
Hom.:
45492
Cov.:
32
AF XY:
0.754
AC XY:
56064
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.548
Gnomad4 AMR
AF:
0.742
Gnomad4 ASJ
AF:
0.887
Gnomad4 EAS
AF:
0.834
Gnomad4 SAS
AF:
0.766
Gnomad4 FIN
AF:
0.757
Gnomad4 NFE
AF:
0.880
Gnomad4 OTH
AF:
0.802
Alfa
AF:
0.862
Hom.:
71690
Bravo
AF:
0.751
Asia WGS
AF:
0.736
AC:
2562
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.0
DANN
Benign
0.30

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12025303; hg19: chr1-112474929; API