rs4842666

Variant names:

• chr12-89547772-T-C
• rs4842666
• ENST00000605233.4:n.7974T>C

Variant summary

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

The ENST00000605233.4(POC1B-AS1):​n.7974T>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 0.163 in 152,126 control chromosomes in the GnomAD database, including 2,320 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 0.16 (2320 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: POC1B-AS1 ENST00000605233.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 21 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605233.4. 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	ENST00000605233.4	TSL:2	n.7974T>C		non_coding_transcript_exon	Exon 3 of 3
	POC1B-AS1	ENST00000716328.1		n.482+4439T>C		intron	N/A
	POC1B-AS1	ENST00000716330.1		n.400-3768T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24798 AN: 152008 Hom.: 2317 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.0806

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.166

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.163 AC: 24811 AN: 152126 Hom.: 2320 Cov.: 32 AF XY: 0.166 AC XY: 12312 AN XY: 74370

African (AFR) AF: 0.132 AC: 5487 AN: 41512

American (AMR) AF: 0.176 AC: 2692 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1758 AN: 5162

South Asian (SAS) AF: 0.354 AC: 1710 AN: 4826

European-Finnish (FIN) AF: 0.0806 AC: 854 AN: 10590

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10926 AN: 67984

Other (OTH) AF: 0.164 AC: 346 AN: 2112

Alfa AF: 0.166 Hom.: 5784

Bravo AF: 0.165

Asia WGS AF: 0.265 AC: 924 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.54
PhyloP100		-2.0

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: rs4842666;

hg19: chr12-89941549;