ENST00000816717.1:n.435C>T

Variant names:

• chr9-37036250-G-A
• rs2282079
• ENST00000816717.1:n.435C>T

Variant summary

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

The ENST00000816717.1(ENSG00000306278):​n.435C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,134 control chromosomes in the GnomAD database, including 277 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 0.055 (277 hom., cov: 32)
• Consequence: ENSG00000306278 ENST00000816717.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 6 publications found

Genes affected

ENSG00000306278 (HGNC:):

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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
ENSG00000306278	ENST00000816717.1	n.435C>T		non_coding_transcript_exon_variant	Exon 1 of 1
EBLN3P	ENST00000816407.1	n.184+1865G>A		intron_variant	Intron 1 of 1
ENSG00000306278	ENST00000816715.1	n.*18C>T		downstream_gene_variant
ENSG00000306278	ENST00000816716.1	n.*3C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8320 AN: 152016 Hom.: 276 Cov.: 32

Gnomad AFR AF: 0.0813

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0233

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0395

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0547 AC: 8327 AN: 152134 Hom.: 277 Cov.: 32 AF XY: 0.0539 AC XY: 4012 AN XY: 74382

African (AFR) AF: 0.0813 AC: 3373 AN: 41488

American (AMR) AF: 0.0620 AC: 948 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3468

East Asian (EAS) AF: 0.114 AC: 591 AN: 5186

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4814

European-Finnish (FIN) AF: 0.0233 AC: 247 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0395 AC: 2688 AN: 67990

Other (OTH) AF: 0.0629 AC: 132 AN: 2100

Alfa AF: 0.0465 Hom.: 258

Bravo AF: 0.0609

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	16
DANN	Benign	0.78
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2282079; hg19: chr9-37036247;