20-44659446-C-T

Variant names:

• chr20-44659446-C-T
• rs6094017
• ENST00000255183.9:n.337+265G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000255183.9(KCNK15-AS1):​n.337+265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,046 control chromosomes in the GnomAD database, including 27,183 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 0.58 (27183 hom., cov: 32)
• Consequence: KCNK15-AS1 ENST00000255183.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 9 publications found

Genes affected

KCNK15-AS1 (HGNC:49901): (KCNK15 and WISP2 antisense RNA 1)

LINC01260 (HGNC:49900): (long intergenic non-protein coding RNA 1260)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01260	NR_034104.1	n.369+265G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNK15-AS1	ENST00000255183.9	n.337+265G>A		intron_variant	Intron 3 of 4	2
KCNK15-AS1	ENST00000415889.2	n.628+265G>A		intron_variant	Intron 4 of 5	5
KCNK15-AS1	ENST00000715845.1	n.631-2395G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88446 AN: 151928 Hom.: 27182 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.582 AC: 88481 AN: 152046 Hom.: 27183 Cov.: 32 AF XY: 0.587 AC XY: 43657 AN XY: 74312

African (AFR) AF: 0.373 AC: 15475 AN: 41450

American (AMR) AF: 0.569 AC: 8693 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2593 AN: 3468

East Asian (EAS) AF: 0.681 AC: 3516 AN: 5166

South Asian (SAS) AF: 0.594 AC: 2859 AN: 4814

European-Finnish (FIN) AF: 0.751 AC: 7958 AN: 10592

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45349 AN: 67970

Other (OTH) AF: 0.609 AC: 1286 AN: 2110

Alfa AF: 0.643 Hom.: 125025

Bravo AF: 0.560

Asia WGS AF: 0.617 AC: 2147 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	2.9
DANN	Benign	0.79
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6094017; hg19: chr20-43288087;