chr19-4237428-A-G

Variant names:

• chr19-4237428-A-G
• rs6613
• NM_005755.3:c.*340A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005755.3(EBI3):​c.*340A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EBI3 NM_005755.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 10 publications found

Genes affected

EBI3 (HGNC:3129): (Epstein-Barr virus induced 3) This gene was identified by its induced expression in B lymphocytes in response Epstein-Barr virus infection. It encodes a secreted glycoprotein belonging to the hematopoietin receptor family, and heterodimerizes with a 28 kDa protein to form interleukin 27 (IL-27). IL-27 regulates T cell and inflammatory responses, in part by activating the Jak/STAT pathway of CD4+ T cells. [provided by RefSeq, Sep 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBI3	NM_005755.3	c.*340A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000221847.6	NP_005746.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBI3	ENST00000221847.6	c.*340A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_005755.3	ENSP00000221847.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 14520 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 7292

African (AFR) AF: 0.00 AC: 0 AN: 510

American (AMR) AF: 0.00 AC: 0 AN: 382

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 674

East Asian (EAS) AF: 0.00 AC: 0 AN: 1018

South Asian (SAS) AF: 0.00 AC: 0 AN: 136

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 554

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 80

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10176

Other (OTH) AF: 0.00 AC: 0 AN: 990

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 873

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		-0.066

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

Other links and lift over

dbSNP: rs6613; hg19: chr19-4237425;