11-2375765-A-G

Variant names:

• chr11-2375765-A-G
• rs708155
• ENST00000427151.1:n.404+1821T>C

Variant summary

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

The ENST00000427151.1(CD81-AS1):​n.404+1821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 151,976 control chromosomes in the GnomAD database, including 47,014 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 0.78 (47014 hom., cov: 31)
• Consequence: CD81-AS1 ENST00000427151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.21
• Publications: 14 publications found

Genes affected

CD81-AS1 (HGNC:49384): (CD81 antisense RNA 1)

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 = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD81-AS1	NR_108080.1	n.407+1821T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD81-AS1	ENST00000427151.1	n.404+1821T>C		intron_variant	Intron 1 of 2	1
CD81-AS1	ENST00000413483.1	n.407+1821T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118762 AN: 151858 Hom.: 46973 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.782 AC: 118851 AN: 151976 Hom.: 47014 Cov.: 31 AF XY: 0.770 AC XY: 57160 AN XY: 74260

African (AFR) AF: 0.837 AC: 34690 AN: 41458

American (AMR) AF: 0.679 AC: 10374 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2891 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2550 AN: 5116

South Asian (SAS) AF: 0.742 AC: 3577 AN: 4822

European-Finnish (FIN) AF: 0.660 AC: 6962 AN: 10548

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55055 AN: 67974

Other (OTH) AF: 0.803 AC: 1692 AN: 2106

Alfa AF: 0.797 Hom.: 45871

Bravo AF: 0.783

Asia WGS AF: 0.668 AC: 2326 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	1.8
DANN	Benign	0.48
PhyloP100		-4.2
PromoterAI		0.042	Neutral

Splicing

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

Other links and lift over

dbSNP: rs708155; hg19: chr11-2396995;