2-223072841-T-G

Position:

• chr2-223072841-T-G

Variant summary

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

The ENST00000488477.2(KCNE4):​n.189+12138T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,212 control chromosomes in the GnomAD database, including 61,351 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 0.90 (61351 hom., cov: 32)
• Consequence: KCNE4 ENST00000488477.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

Genes affected

KCNE4 (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 = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124907986	XR_007088096.1	n.109+12138T>G		intron_variant
LOC124907986	XR_007088097.1	n.110-3646T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNE4	ENST00000488477.2	n.189+12138T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136433 AN: 152094 Hom.: 61309 Cov.: 32

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.897 AC: 136531 AN: 152212 Hom.: 61351 Cov.: 32 AF XY: 0.899 AC XY: 66907 AN XY: 74414

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.860

Alfa AF: 0.875 Hom.: 95677

Bravo AF: 0.892

Asia WGS AF: 0.915 AC: 3183 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	5.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs960246; hg19: chr2-223937559;