rs1064273

Variant names:

• chr21-38301377-C-T
• rs1064273
• NM_170736.3:c.*988C>T

Variant summary

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

The NM_170736.3(KCNJ15):​c.*988C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 166,932 control chromosomes in the GnomAD database, including 19,816 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 0.46 (17927 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1889 hom.)
• Consequence: KCNJ15 NM_170736.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 10 publications found

Genes affected

KCNJ15 (HGNC:6261): (potassium inwardly rectifying channel subfamily J member 15) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein has a greater tendency to allow potassium to flow into a cell rather than out of a cell. Eight transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNJ15	NM_170736.3	c.*988C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000398938.7	NP_733932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNJ15	ENST00000398938.7	c.*988C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_170736.3	ENSP00000381911.2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70275 AN: 151930 Hom.: 17931 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.464

GnomAD4 exome AF: 0.504 AC: 7507 AN: 14884 Hom.: 1889 Cov.: 0 AF XY: 0.505 AC XY: 3569 AN XY: 7070

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.504 AC: 7404 AN: 14696

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 42 AN: 84

Other (OTH) AF: 0.600 AC: 54 AN: 90

GnomAD4 genome AF: 0.462 AC: 70286 AN: 152048 Hom.: 17927 Cov.: 33 AF XY: 0.458 AC XY: 34025 AN XY: 74310

African (AFR) AF: 0.256 AC: 10632 AN: 41464

American (AMR) AF: 0.499 AC: 7636 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1490 AN: 5166

South Asian (SAS) AF: 0.384 AC: 1852 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5402 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39985 AN: 67964

Other (OTH) AF: 0.461 AC: 976 AN: 2116

Alfa AF: 0.542 Hom.: 91249

Bravo AF: 0.453

Asia WGS AF: 0.333 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.65
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1064273; hg19: chr21-39673299;