rs11696845

Positions:

• chr20-44742679-C-T

Variant summary

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

The NR_132377.1(KCNK15-AS1):​n.263+3286G>A variant causes a intron, non coding transcript 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 NR_132377.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
KCNK15-AS1	NR_132377.1	n.263+3286G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNK15-AS1	ENST00000445420.5	n.31+3286G>A		intron_variant, non_coding_transcript_variant		2
KCNK15-AS1	ENST00000427303.2	n.57+3286G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.338

Alfa AF: 0.356 Hom.: 3620

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696845; hg19: chr20-43371320;