10-30109862-T-G

Variant names:

• chr10-30109862-T-G
• rs2505115
• NM_001350022.2:c.-182+5505A>C

Variant summary

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

The NM_001350022.2(JCAD):​c.-182+5505A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 151,636 control chromosomes in the GnomAD database, including 57,967 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 0.87 (57967 hom., cov: 29)
• Consequence: JCAD NM_001350022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.64
• Publications: 4 publications found

Genes affected

JCAD (HGNC:29283): (junctional cadherin 5 associated) This gene encodes an endothelial cell-to-cell junction protein. Naturally occurring mutations in this gene are associated with coronary artery disease, late onset alzheimer disease, and emphysema distribution. [provided by RefSeq, Mar 2017]

ENSG00000296831 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350022.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JCAD	NM_001350022.2		c.-182+5505A>C		intron	N/A	NP_001336951.1
	JCAD	NM_001350021.2		c.-514+5505A>C		intron	N/A	NP_001336950.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JCAD	ENST00000465712.1	TSL:3	n.128+5505A>C		intron	N/A
	ENSG00000296831	ENST00000742833.1		n.176-786T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132093 AN: 151518 Hom.: 57896 Cov.: 29

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.872 AC: 132226 AN: 151636 Hom.: 57967 Cov.: 29 AF XY: 0.866 AC XY: 64197 AN XY: 74102

African (AFR) AF: 0.918 AC: 37967 AN: 41372

American (AMR) AF: 0.911 AC: 13899 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2962 AN: 3460

East Asian (EAS) AF: 0.687 AC: 3507 AN: 5104

South Asian (SAS) AF: 0.713 AC: 3404 AN: 4776

European-Finnish (FIN) AF: 0.789 AC: 8315 AN: 10540

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59437 AN: 67834

Other (OTH) AF: 0.872 AC: 1832 AN: 2100

Alfa AF: 0.879 Hom.: 119559

Bravo AF: 0.885

Asia WGS AF: 0.722 AC: 2512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.64
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs2505115; hg19: chr10-30398791;