chr2-18208949-C-A

Position:

• chr2-18208949-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.925 in 152,302 control chromosomes in the GnomAD database, including 65,288 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 0.93 (65288 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.18208949C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNS3	ENST00000465292.5	n.424+38441C>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140820 AN: 152184 Hom.: 65259 Cov.: 33

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.925 AC: 140902 AN: 152302 Hom.: 65288 Cov.: 33 AF XY: 0.923 AC XY: 68751 AN XY: 74474

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.932

Alfa AF: 0.946 Hom.: 94310

Bravo AF: 0.924

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2345518; hg19: chr2-18390215;