1-160088822-C-T

Position:

• chr1-160088822-C-T

Variant summary

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

The NM_004983.3(KCNJ9):​c.*1005C>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 0.302 in 152,130 control chromosomes in the GnomAD database, including 7,151 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 0.30 (7143 hom., cov: 32)
  • Exomes 𝑓: 0.28 (8 hom.)
• Consequence: KCNJ9 NM_004983.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

KCNJ9 (HGNC:6270): (potassium inwardly rectifying channel subfamily J member 9) 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, which has a greater tendency to allow potassium to flow into a cell rather than out of a cell, is controlled by G-proteins. It associates with another G-protein-activated potassium channel to form a heteromultimeric pore-forming complex. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNJ9	NM_004983.3	c.*1005C>T		3_prime_UTR_variant	3/3	ENST00000368088.4	NP_004974.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNJ9	ENST00000368088.4	c.*1005C>T		3_prime_UTR_variant	3/3	1	NM_004983.3	ENSP00000357067.3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45857 AN: 151908 Hom.: 7145 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.279 AC: 29 AN: 104 Hom.: 8 Cov.: 0 AF XY: 0.292 AC XY: 21 AN XY: 72

Gnomad4 AFR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.280

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.302 AC: 45858 AN: 152026 Hom.: 7143 Cov.: 32 AF XY: 0.303 AC XY: 22541 AN XY: 74308

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.292

Alfa AF: 0.306 Hom.: 1202

Bravo AF: 0.288

Asia WGS AF: 0.217 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494211; hg19: chr1-160058612;