rs16928120

chr11-2329512-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413483.1(CD81-AS1):n.697G>C variant causes a non coding transcript exon 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 ENST00000413483.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CD81-AS1	NR_108080.1	n.619+51G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD81-AS1	ENST00000413483.1	n.697G>C		non_coding_transcript_exon_variant	3/3	2
CD81-AS1	ENST00000427151.1	n.616+51G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19846 AN: 151888 Hom.: 1790 Cov.: 32

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: 3 AN: 40 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.131 AC: 19892 AN: 152004 Hom.: 1795 Cov.: 32 AF XY: 0.128 AC XY: 9539 AN XY: 74316

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0762

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0755

Gnomad4 OTH AF: 0.132

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
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16928120; hg19: chr11-2350742;