9-37037979-T-G

Variant names:

• chr9-37037979-T-G
• rs1329568
• ENST00000816407.1:n.184+3594T>G

Variant summary

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

The ENST00000816407.1(EBLN3P):​n.184+3594T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,328 control chromosomes in the GnomAD database, including 66,603 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 0.93 (66603 hom., cov: 36)
• Consequence: EBLN3P ENST00000816407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 13 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816407.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBLN3P	ENST00000816407.1		n.184+3594T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141717 AN: 152210 Hom.: 66568 Cov.: 36

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.931 AC: 141803 AN: 152328 Hom.: 66603 Cov.: 36 AF XY: 0.932 AC XY: 69398 AN XY: 74496

African (AFR) AF: 0.785 AC: 32603 AN: 41532

American (AMR) AF: 0.961 AC: 14718 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3405 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5031 AN: 5188

South Asian (SAS) AF: 0.989 AC: 4777 AN: 4832

European-Finnish (FIN) AF: 0.979 AC: 10400 AN: 10626

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67652 AN: 68048

Other (OTH) AF: 0.957 AC: 2024 AN: 2116

Alfa AF: 0.974 Hom.: 218419

Bravo AF: 0.921

Asia WGS AF: 0.968 AC: 3366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1329568; hg19: chr9-37037976;