2-17979049-C-T

Position:

• chr2-17979049-C-T

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 0.0588 in 152,234 control chromosomes in the GnomAD database, including 658 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 0.059 (658 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17979049C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNS3	ENST00000465292.5	n.305+61178C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0587 AC: 8930 AN: 152118 Hom.: 652 Cov.: 32

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0588 AC: 8951 AN: 152234 Hom.: 658 Cov.: 32 AF XY: 0.0665 AC XY: 4946 AN XY: 74428

Gnomad4 AFR AF: 0.0501

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0377 Hom.: 141

Bravo AF: 0.0638

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495674; hg19: chr2-18160315;