12-89548613-A-G

Variant names:

• chr12-89548613-A-G
• rs11105328
• ENST00000716328.1:n.482+5280A>G

Variant summary

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

The ENST00000716328.1(POC1B-AS1):​n.482+5280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,118 control chromosomes in the GnomAD database, including 1,855 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 0.15 (1855 hom., cov: 32)
• Consequence: POC1B-AS1 ENST00000716328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• Publications: 16 publications found

Genes affected

POC1B-AS1 (HGNC:52949): (POC1B antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POC1B-AS1	ENST00000716328.1	n.482+5280A>G		intron_variant	Intron 2 of 4
POC1B-AS1	ENST00000716330.1	n.400-2927A>G		intron_variant	Intron 2 of 4
POC1B-AS1	ENST00000716331.1	n.381-2927A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22452 AN: 152000 Hom.: 1852 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.148 AC: 22461 AN: 152118 Hom.: 1855 Cov.: 32 AF XY: 0.148 AC XY: 10995 AN XY: 74358

African (AFR) AF: 0.131 AC: 5420 AN: 41502

American (AMR) AF: 0.113 AC: 1730 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1051 AN: 5162

South Asian (SAS) AF: 0.315 AC: 1513 AN: 4808

European-Finnish (FIN) AF: 0.0743 AC: 787 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10690 AN: 67992

Other (OTH) AF: 0.147 AC: 311 AN: 2114

Alfa AF: 0.156 Hom.: 7755

Bravo AF: 0.146

Asia WGS AF: 0.184 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.9
DANN	Benign	0.78
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs11105328; hg19: chr12-89942390;