19-47758358-G-C

Variant names:

• chr19-47758358-G-C
• rs11669775
• ENST00000602048.1:n.299-1081C>G

Variant summary

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

The ENST00000602048.1(NOP53-AS1):​n.299-1081C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (30909 hom., cov: 20)
• Consequence: NOP53-AS1 ENST00000602048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

Genes affected

NOP53-AS1 (HGNC:51587): (NOP53 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 (SAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOP53-AS1	NR_132382.1	n.299-1081C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOP53-AS1	ENST00000602048.1	n.299-1081C>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.647 AC: 92408 AN: 142770 Hom.: 30906 Cov.: 20

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.647 AC: 92448 AN: 142872 Hom.: 30909 Cov.: 20 AF XY: 0.648 AC XY: 44587 AN XY: 68800

African (AFR) AF: 0.459 AC: 17482 AN: 38124

American (AMR) AF: 0.706 AC: 9753 AN: 13816

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2212 AN: 3402

East Asian (EAS) AF: 0.778 AC: 3708 AN: 4768

South Asian (SAS) AF: 0.805 AC: 3482 AN: 4326

European-Finnish (FIN) AF: 0.688 AC: 6262 AN: 9100

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.717 AC: 47491 AN: 66224

Other (OTH) AF: 0.629 AC: 1222 AN: 1942

Alfa AF: 0.577 Hom.: 1775

Bravo AF: 0.636

Asia WGS AF: 0.768 AC: 2667 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11669775; hg19: chr19-48261615;