rs3862227

Variant names:

• chr1-43255323-A-G
• rs3862227
• ENST00000461557.2:n.108+6519T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-43255323-A-G
• chr1-43255323-A-T

Variant summary

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

The ENST00000466927.5(EBNA1BP2):​n.69+6519T>C 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 152,042 control chromosomes in the GnomAD database, including 10,271 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 (10271 hom., cov: 32)
• Consequence: EBNA1BP2 ENST00000466927.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942

Genes affected

EBNA1BP2 (HGNC:15531): (EBNA1 binding protein 2) Enables RNA binding activity. Predicted to be involved in rRNA processing and ribosomal large subunit biogenesis. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBNA1BP2	ENST00000461557.2	n.108+6519T>C		intron_variant	Intron 2 of 8	5
EBNA1BP2	ENST00000466927.5	n.69+6519T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51901 AN: 151924 Hom.: 10261 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.341 AC: 51905 AN: 152042 Hom.: 10271 Cov.: 32 AF XY: 0.346 AC XY: 25700 AN XY: 74306

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.344

Alfa AF: 0.352 Hom.: 1979

Bravo AF: 0.326

Asia WGS AF: 0.523 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3862227; hg19: chr1-43720994;