rs10508642

Variant names:

• chr10-22213278-T-A
• rs10508642
• NM_001394757.1:c.-168-313A>T

Variant summary

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

The NM_001394757.1(EBLN1):​c.-168-313A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,272 control chromosomes in the GnomAD database, including 653 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 0.063 (653 hom., cov: 32)
• Consequence: EBLN1 NM_001394757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 3 publications found

Genes affected

EBLN1 (HGNC:39430): (endogenous Bornavirus like nucleoprotein 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394757.1. 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
	EBLN1	NM_001394757.1	MANE Select	c.-168-313A>T		intron	N/A	NP_001381686.1	P0CF75

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBLN1	ENST00000422359.3	TSL:6 MANE Select	c.-168-313A>T		intron	N/A	ENSP00000473842.1	P0CF75
	EBLN1	ENST00000939589.1		c.-44-3251A>T		intron	N/A	ENSP00000609648.1

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9585 AN: 152154 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0633 AC: 9633 AN: 152272 Hom.: 653 Cov.: 32 AF XY: 0.0606 AC XY: 4514 AN XY: 74474

African (AFR) AF: 0.170 AC: 7058 AN: 41544

American (AMR) AF: 0.0325 AC: 497 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3468

East Asian (EAS) AF: 0.00540 AC: 28 AN: 5186

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4826

European-Finnish (FIN) AF: 0.0139 AC: 147 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0201 AC: 1365 AN: 68018

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0452 Hom.: 44

Bravo AF: 0.0694

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.17
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10508642; hg19: chr10-22502207;