chr19-43641391-T-A

Variant names:

• chr19-43641391-T-A
• rs4803648
• ENST00000830541.1:n.91+1374T>A

Variant summary

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

The ENST00000830541.1(ENSG00000308028):​n.91+1374T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,126 control chromosomes in the GnomAD database, including 11,460 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 0.34 (11460 hom., cov: 31)
• Consequence: ENSG00000308028 ENST00000830541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 10 publications found

Genes affected

ENSG00000308028 (HGNC:):

CADM4 (HGNC:30825): (cell adhesion molecule 4) Enables vascular endothelial growth factor receptor 2 binding activity. Involved in several processes, including negative regulation of protein phosphorylation; regulation of Rac protein signal transduction; and regulation of wound healing. Located in cell leading edge and cell-cell contact zone. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830541.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308028	ENST00000830541.1		n.91+1374T>A		intron	N/A
	ENSG00000308028	ENST00000830542.1		n.50+1309T>A		intron	N/A
	ENSG00000308028	ENST00000830543.1		n.101+1067T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51779 AN: 152008 Hom.: 11425 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.341 AC: 51866 AN: 152126 Hom.: 11460 Cov.: 31 AF XY: 0.337 AC XY: 25051 AN XY: 74394

African (AFR) AF: 0.629 AC: 26089 AN: 41488

American (AMR) AF: 0.335 AC: 5120 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1440 AN: 5164

South Asian (SAS) AF: 0.168 AC: 811 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10618

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14757 AN: 67978

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.298 Hom.: 922

Bravo AF: 0.372

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.43
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4803648; hg19: chr19-44145543;