rs10508641

Variant names:

• chr10-22212605-T-C
• rs10508641
• NM_001394757.1:c.-45+237A>G

Variant summary

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

The NM_001394757.1(EBLN1):​c.-45+237A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 152,064 control chromosomes in the GnomAD database, including 722 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 0.064 (722 hom., cov: 31)
• Consequence: EBLN1 NM_001394757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 0 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBLN1	NM_001394757.1	c.-45+237A>G		intron_variant	Intron 2 of 2	ENST00000422359.3	NP_001381686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBLN1	ENST00000422359.3	c.-45+237A>G		intron_variant	Intron 2 of 2	6	NM_001394757.1	ENSP00000473842.1

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9704 AN: 151946 Hom.: 721 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00849

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0638 AC: 9709 AN: 152064 Hom.: 722 Cov.: 31 AF XY: 0.0632 AC XY: 4699 AN XY: 74348

African (AFR) AF: 0.181 AC: 7481 AN: 41422

American (AMR) AF: 0.0306 AC: 467 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0237 AC: 114 AN: 4816

European-Finnish (FIN) AF: 0.00849 AC: 90 AN: 10596

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1307 AN: 67996

Other (OTH) AF: 0.0493 AC: 104 AN: 2110

Alfa AF: 0.0372 Hom.: 71

Bravo AF: 0.0701

Asia WGS AF: 0.0300 AC: 106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10508641; hg19: chr10-22501534;