rs1597167

Positions:

• chr2-223179532-A-G
• chr2-223179532-A-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 0.667 in 152,034 control chromosomes in the GnomAD database, including 34,641 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 0.67 (34641 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.223179532A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNE4	ENST00000488477.2	n.190-13537A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101261 AN: 151916 Hom.: 34602 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.667 AC: 101346 AN: 152034 Hom.: 34641 Cov.: 31 AF XY: 0.661 AC XY: 49140 AN XY: 74332

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.632

Alfa AF: 0.616 Hom.: 59106

Bravo AF: 0.671

Asia WGS AF: 0.594 AC: 2063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1597167; hg19: chr2-224044250;