chr14-59492132-C-T

Position:

• chr14-59492132-C-T

Variant summary

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

The NM_016475.5(JKAMP):​c.252-2886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,744 control chromosomes in the GnomAD database, including 5,696 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 (5696 hom., cov: 32)
• Consequence: JKAMP NM_016475.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

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]

L3HYPDH (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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/exons	MANE	Protein	UniProt
JKAMP	NM_016475.5	c.252-2886C>T		intron_variant		ENST00000616435.5	NP_057559.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JKAMP	ENST00000616435.5	c.252-2886C>T		intron_variant		5	NM_016475.5	ENSP00000479775	P1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40390 AN: 151626 Hom.: 5686 Cov.: 32

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: 0.127

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.266

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.267 AC: 40450 AN: 151744 Hom.: 5696 Cov.: 32 AF XY: 0.265 AC XY: 19633 AN XY: 74136

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.264

Alfa AF: 0.245 Hom.: 962

Bravo AF: 0.280

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.74

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: rs2182836; hg19: chr14-59958850;