chr9-37038261-G-T

Variant names:

• chr9-37038261-G-T
• rs4256662
• ENST00000816407.1:n.184+3876G>T

Variant summary

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

The ENST00000816407.1(EBLN3P):​n.184+3876G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,288 control chromosomes in the GnomAD database, including 47,604 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 0.76 (47604 hom., cov: 36)
• Consequence: EBLN3P ENST00000816407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 2 publications found

Genes affected

EBLN3P (HGNC:50682): (endogenous Bornavirus like nucleoprotein 3, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.909 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
EBLN3P	ENST00000816407.1	n.184+3876G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115793 AN: 152170 Hom.: 47586 Cov.: 36

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.761 AC: 115835 AN: 152288 Hom.: 47604 Cov.: 36 AF XY: 0.764 AC XY: 56924 AN XY: 74484

African (AFR) AF: 0.416 AC: 17294 AN: 41528

American (AMR) AF: 0.836 AC: 12800 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3101 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3652 AN: 5184

South Asian (SAS) AF: 0.909 AC: 4390 AN: 4830

European-Finnish (FIN) AF: 0.897 AC: 9530 AN: 10620

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62281 AN: 68030

Other (OTH) AF: 0.800 AC: 1692 AN: 2114

Alfa AF: 0.863 Hom.: 107627

Bravo AF: 0.737

Asia WGS AF: 0.796 AC: 2769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.53
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs4256662; hg19: chr9-37038258;