rs10858911

Variant names:

• chr12-89569364-G-A
• rs10858911
• ENST00000716328.1:n.629-5312G>A

Variant summary

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

The ENST00000716328.1(POC1B-AS1):​n.629-5312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,768 control chromosomes in the GnomAD database, including 21,497 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 0.52 (21497 hom., cov: 31)
• Consequence: POC1B-AS1 ENST00000716328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716328.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POC1B-AS1	ENST00000716328.1		n.629-5312G>A		intron	N/A
	POC1B-AS1	ENST00000716330.1		n.539-5312G>A		intron	N/A
	POC1B-AS1	ENST00000716331.1		n.665+8089G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78789 AN: 151652 Hom.: 21459 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.520 AC: 78872 AN: 151768 Hom.: 21497 Cov.: 31 AF XY: 0.512 AC XY: 38000 AN XY: 74184

African (AFR) AF: 0.672 AC: 27775 AN: 41334

American (AMR) AF: 0.380 AC: 5795 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1555 AN: 5142

South Asian (SAS) AF: 0.507 AC: 2442 AN: 4812

European-Finnish (FIN) AF: 0.420 AC: 4424 AN: 10526

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33536 AN: 67922

Other (OTH) AF: 0.478 AC: 1005 AN: 2102

Alfa AF: 0.496 Hom.: 7564

Bravo AF: 0.522

Asia WGS AF: 0.365 AC: 1273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10858911;

hg19: chr12-89963141;