chr9-37066620-T-C

Variant names:

• chr9-37066620-T-C
• rs10973184
• ENST00000816407.1:n.185-20048T>C

Variant summary

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

The ENST00000816407.1(EBLN3P):​n.185-20048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,122 control chromosomes in the GnomAD database, including 2,199 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 0.16 (2199 hom., cov: 32)
• Consequence: EBLN3P ENST00000816407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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.185-20048T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23663 AN: 152000 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.156 AC: 23705 AN: 152122 Hom.: 2199 Cov.: 32 AF XY: 0.158 AC XY: 11730 AN XY: 74364

African (AFR) AF: 0.249 AC: 10340 AN: 41462

American (AMR) AF: 0.0964 AC: 1473 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.0954 AC: 495 AN: 5190

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1560 AN: 10594

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7639 AN: 67978

Other (OTH) AF: 0.153 AC: 324 AN: 2114

Alfa AF: 0.143 Hom.: 332

Bravo AF: 0.153

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.29
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10973184; hg19: chr9-37066617;