rs11696845

Variant names:

• chr20-44742679-C-T
• rs11696845
• ENST00000427303.2:n.57+3286G>A

Variant summary

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

The ENST00000427303.2(KCNK15-AS1):​n.57+3286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,132 control chromosomes in the GnomAD database, including 9,047 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 0.32 (9047 hom., cov: 32)
• Consequence: KCNK15-AS1 ENST00000427303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 10 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNK15-AS1	NR_132377.1	n.263+3286G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNK15-AS1	ENST00000427303.2	n.57+3286G>A		intron_variant	Intron 1 of 5	5
KCNK15-AS1	ENST00000445420.6	n.310+3286G>A		intron_variant	Intron 1 of 2	2
KCNK15-AS1	ENST00000715845.1	n.398+3286G>A		intron_variant	Intron 1 of 3
KCNK15-AS1	ENST00000798954.1	n.222+3286G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 49016 AN: 152014 Hom.: 9043 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.322 AC: 49023 AN: 152132 Hom.: 9047 Cov.: 32 AF XY: 0.322 AC XY: 23953 AN XY: 74368

African (AFR) AF: 0.138 AC: 5714 AN: 41532

American (AMR) AF: 0.338 AC: 5169 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1828 AN: 5170

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4467 AN: 10572

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27412 AN: 67958

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.356 Hom.: 4373

Bravo AF: 0.310

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11696845; hg19: chr20-43371320;