rs4234723

Variant names:

• chr4-6218202-A-G
• rs4234723
• ENST00000508601.2:n.208-8724A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000508601.2(ENSG00000290803):​n.208-8724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,976 control chromosomes in the GnomAD database, including 19,615 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 0.51 (19615 hom., cov: 32)
• Consequence: ENSG00000290803 ENST00000508601.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 7 publications found

Genes affected

ENSG00000290803 (HGNC:):

JAKMIP1-DT (HGNC:27728): (JAKMIP1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP1-DT	NR_037863.1	n.208-8724A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290803	ENST00000508601.2	n.208-8724A>G		intron_variant	Intron 1 of 4	2
ENSG00000290803	ENST00000776984.1	n.156-8724A>G		intron_variant	Intron 1 of 4
ENSG00000290803	ENST00000776985.1	n.160-8724A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77012 AN: 151858 Hom.: 19602 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.507 AC: 77074 AN: 151976 Hom.: 19615 Cov.: 32 AF XY: 0.509 AC XY: 37790 AN XY: 74260

African (AFR) AF: 0.523 AC: 21675 AN: 41438

American (AMR) AF: 0.461 AC: 7043 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2354 AN: 5162

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4814

European-Finnish (FIN) AF: 0.563 AC: 5937 AN: 10538

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34483 AN: 67974

Other (OTH) AF: 0.508 AC: 1075 AN: 2116

Alfa AF: 0.504 Hom.: 7429

Bravo AF: 0.500

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.64
PhyloP100		0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4234723; hg19: chr4-6219929;