chr5-147708782-A-G

Position:

• chr5-147708782-A-G

Variant summary

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

The NM_001270941.2(JAKMIP2):​c.-148-36828T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,114 control chromosomes in the GnomAD database, including 4,363 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 0.23 (4363 hom., cov: 32)
• Consequence: JAKMIP2 NM_001270941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

JAKMIP2 (HGNC:29067): (janus kinase and microtubule interacting protein 2) The protein encoded by this gene is reported to be a component of the Golgi matrix. It may act as a golgin protein by negatively regulating transit of secretory cargo and by acting as a structural scaffold of the Golgi. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAKMIP2	NM_001270941.2	c.-148-36828T>C		intron_variant		ENST00000616793.5	NP_001257870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAKMIP2	ENST00000616793.5	c.-148-36828T>C		intron_variant		5	NM_001270941.2	ENSP00000479248	P1
JAKMIP2	ENST00000265272.9	c.-148-36828T>C		intron_variant		1		ENSP00000265272
JAKMIP2	ENST00000507386.5	c.-148-36828T>C		intron_variant		1		ENSP00000421398
JAKMIP2	ENST00000333010.6	c.4-47337T>C		intron_variant		2		ENSP00000328989

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35364 AN: 151996 Hom.: 4349 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.233 AC: 35413 AN: 152114 Hom.: 4363 Cov.: 32 AF XY: 0.238 AC XY: 17709 AN XY: 74368

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.212

Alfa AF: 0.216 Hom.: 446

Bravo AF: 0.237

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.49

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: rs7713108; hg19: chr5-147088345;