rs917901

Variant summary

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

The NM_012281.3(KCND2):​c.1115+180910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,192 control chromosomes in the GnomAD database, including 828 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 0.10 ( 828 hom., cov: 32)

Consequence

KCND2
NM_012281.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.717
Variant links:
Genes affected
KCND2 (HGNC:6238): (potassium voltage-gated channel subfamily D member 2) 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 mediates a rapidly inactivating, A-type outward potassium current which is not under the control of the N terminus as it is in Shaker channels. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCND2NM_012281.3 linkuse as main transcriptc.1115+180910C>T intron_variant ENST00000331113.9 NP_036413.1 Q9NZV8A4D0V9
KCND2XM_047420346.1 linkuse as main transcriptc.1115+180910C>T intron_variant XP_047276302.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCND2ENST00000331113.9 linkuse as main transcriptc.1115+180910C>T intron_variant 1 NM_012281.3 ENSP00000333496.4 Q9NZV8

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15535
AN:
152074
Hom.:
830
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.106
Gnomad AMI
AF:
0.138
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.0372
Gnomad SAS
AF:
0.0456
Gnomad FIN
AF:
0.0730
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.105
Gnomad OTH
AF:
0.109
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15537
AN:
152192
Hom.:
828
Cov.:
32
AF XY:
0.0979
AC XY:
7288
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.106
Gnomad4 AMR
AF:
0.132
Gnomad4 ASJ
AF:
0.115
Gnomad4 EAS
AF:
0.0371
Gnomad4 SAS
AF:
0.0458
Gnomad4 FIN
AF:
0.0730
Gnomad4 NFE
AF:
0.105
Gnomad4 OTH
AF:
0.111
Alfa
AF:
0.100
Hom.:
82
Bravo
AF:
0.108
Asia WGS
AF:
0.0930
AC:
324
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.7
DANN
Benign
0.23

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: rs917901; hg19: chr7-120096711; API