dbSNP rs16928120: CD81-AS1:n.616+51G>C (chr11-2329512-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000427151.1(CD81-AS1):n.616+51G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,044 control chromosomes in the GnomAD database, including 1,795 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 0.13 ( 1795 hom., cov: 32)

Exomes 𝑓: 0.075 ( 0 hom. )

Consequence

CD81-AS1
ENST00000427151.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.659

Publications

3 publications found

Variant links:

Genes affected

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

CD81-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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
CD81-AS1	NR_108080.1 link	n.619+51G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD81-AS1	ENST00000427151.1 link	n.616+51G>C		intron_variant	Intron 2 of 2	1
CD81-AS1	ENST00000413483.1 link	n.697G>C		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19846

AN:

151888

Hom.:

1790

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.0762

Gnomad EAS

AF:

0.162

Gnomad SAS

AF:

0.0977

Gnomad FIN

AF:

0.0501

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0755

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.0750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.136

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.150

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.131

AC:

19892

AN:

152004

Hom.:

1795

Cov.:

AF XY:

0.128

AC XY:

9539

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.249

AC:

10289

AN:

41382

American (AMR)

AF:

0.129

AC:

1965

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0762

AC:

264

AN:

3466

East Asian (EAS)

AF:

0.162

AC:

835

AN:

5166

South Asian (SAS)

AF:

0.0980

AC:

472

AN:

4818

European-Finnish (FIN)

AF:

0.0501

AC:

530

AN:

10584

Middle Eastern (MID)

AF:

0.0890

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0755

AC:

5135

AN:

68004

Other (OTH)

AF:

0.132

AC:

279

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

833

1666

2499

3332

4165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.106

Hom.:

159

Bravo

AF:

0.143

Asia WGS

AF:

0.165

AC:

573

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.2

(source)

DANN

Benign

0.69

PhyloP100

0.66

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over