Genetic Variant JKAMP:n.1213T>G (chr14-59504321-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000602482.5(JKAMP):n.1213T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 461,498 control chromosomes in the GnomAD database, including 16,811 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 0.27 ( 5707 hom., cov: 32)

Exomes 𝑓: 0.26 ( 11104 hom. )

Consequence

JKAMP
ENST00000602482.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.528

Publications

15 publications found

Variant links:

Genes affected

JKAMP (HGNC:20184): (JNK1/MAPK8 associated membrane protein) Enables ubiquitin protein ligase binding activity. Involved in ubiquitin-dependent ERAD pathway. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

JKAMP links:

ENSG00000258782 (HGNC:):

ENSG00000258782 links:

L3HYPDH (HGNC:20488): (trans-L-3-hydroxyproline dehydratase) The protein encoded by this gene is a dehydratase that converts trans-3-hydroxy-L-proline to delta(1)-pyrroline-2-carboxylate. This enzyme may function to degrade dietary proteins that contain trans-3-hydroxy-L-proline as well as other proteins such as collagen IV. The encoded protein can be converted to an epimerase by changing a threonine to a cysteine at a catalytic site. [provided by RefSeq, Sep 2016]

L3HYPDH links:

CCDC175 (HGNC:19847): (coiled-coil domain containing 175)

CCDC175 links:

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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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JKAMP	NM_016475.5 link	c.*249T>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000616435.5	NP_057559.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JKAMP	ENST00000616435.5 link	c.*249T>G		3_prime_UTR_variant	Exon 7 of 7	5	NM_016475.5	ENSP00000479775.2		Q9P055-4

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40437

AN:

151980

Hom.:

5696

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.400

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.259

AC:

79996

AN:

309398

Hom.:

11104

Cov.:

AF XY:

0.266

AC XY:

42856

AN XY:

161096

show subpopulations

African (AFR)

AF:

0.318

AC:

2908

AN:

9158

American (AMR)

AF:

0.335

AC:

3723

AN:

11122

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

2921

AN:

10440

East Asian (EAS)

AF:

0.191

AC:

4320

AN:

22590

South Asian (SAS)

AF:

0.425

AC:

10325

AN:

24304

European-Finnish (FIN)

AF:

0.133

AC:

2538

AN:

19052

Middle Eastern (MID)

AF:

0.351

AC:

510

AN:

1454

European-Non Finnish (NFE)

AF:

0.248

AC:

47781

AN:

192318

Other (OTH)

AF:

0.262

AC:

4970

AN:

18960

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2720

5439

8159

10878

13598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.266

AC:

40498

AN:

152100

Hom.:

5707

Cov.:

AF XY:

0.264

AC XY:

19644

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.316

AC:

13119

AN:

41502

American (AMR)

AF:

0.317

AC:

4844

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

924

AN:

3464

East Asian (EAS)

AF:

0.181

AC:

938

AN:

5178

South Asian (SAS)

AF:

0.400

AC:

1917

AN:

4796

European-Finnish (FIN)

AF:

0.125

AC:

1324

AN:

10606

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.244

AC:

16588

AN:

67972

Other (OTH)

AF:

0.266

AC:

560

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1483

2967

4450

5934

7417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.258

Hom.:

16131

Bravo

AF:

0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.5

(source)

DANN

Benign

0.76

PhyloP100

-0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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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14-59504321-T-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over