Genetic Variant NM_004983.3:c.*1005C>T (chr1-160088822-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0150

Publications

7 publications found

Variant links:

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]

KCNJ9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004983.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNJ9	NM_004983.3	MANE Select	c.*1005C>T		3_prime_UTR	Exon 3 of 3	NP_004974.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KCNJ9	ENST00000368088.4	TSL:1 MANE Select	c.*1005C>T	3_prime_UTR	Exon 3 of 3	ENSP00000357067.3	Q92806
KCNJ9	ENST00000864453.1		c.*1005C>T	3_prime_UTR	Exon 4 of 4	ENSP00000534512.1
KCNJ9	ENST00000864454.1		c.*1005C>T	3_prime_UTR	Exon 3 of 3	ENSP00000534513.1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45857

AN:

151908

Hom.:

7145

Cov.:

show subpopulations

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:

AN:

104

Hom.:

Cov.:

AF XY:

0.292

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.280

AC:

AN:

Other (OTH)

AF:

0.286

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.567

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.302

AC:

45858

AN:

152026

Hom.:

7143

Cov.:

AF XY:

0.303

AC XY:

22541

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.253

AC:

10472

AN:

41438

American (AMR)

AF:

0.261

AC:

3989

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.377

AC:

1306

AN:

3468

East Asian (EAS)

AF:

0.276

AC:

1426

AN:

5158

South Asian (SAS)

AF:

0.223

AC:

1077

AN:

4832

European-Finnish (FIN)

AF:

0.409

AC:

4324

AN:

10564

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.329

AC:

22362

AN:

67964

Other (OTH)

AF:

0.292

AC:

615

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1580

3160

4740

6320

7900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.302

Hom.:

2399

Bravo

AF:

0.288

Asia WGS

AF:

0.217

AC:

759

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.4

(source)

DANN

Benign

0.84

PhyloP100

-0.015

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over