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.

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	ENST00000605233.4	n.7974T>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
POC1B-AS1	ENST00000716328.1	n.482+4439T>C		intron_variant	Intron 2 of 4
POC1B-AS1	ENST00000716330.1	n.400-3768T>C		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs4842666; hg19: chr12-89941549;