rs16869658

Variant names:

• chr8-102621534-G-A
• rs16869658
• ENST00000521750.3:n.798C>T

Variant summary

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

The ENST00000521750.3(POU5F1P2):​n.798C>T 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 0.209 in 173,968 control chromosomes in the GnomAD database, including 3,953 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 0.21 (3431 hom., cov: 32)
  • Exomes 𝑓: 0.21 (522 hom.)
• Consequence: POU5F1P2 ENST00000521750.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 2 publications found

Genes affected

POU5F1P2 (HGNC:33309): (POU class 5 homeobox 1 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521750.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU5F1P2	ENST00000521750.3	TSL:6	n.798C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31795 AN: 152024 Hom.: 3424 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.205 AC: 4484 AN: 21826 Hom.: 522 Cov.: 0 AF XY: 0.199 AC XY: 2158 AN XY: 10866

African (AFR) AF: 0.294 AC: 20 AN: 68

American (AMR) AF: 0.107 AC: 25 AN: 234

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 32 AN: 174

East Asian (EAS) AF: 0.195 AC: 23 AN: 118

South Asian (SAS) AF: 0.243 AC: 403 AN: 1658

European-Finnish (FIN) AF: 0.202 AC: 2611 AN: 12952

Middle Eastern (MID) AF: 0.146 AC: 7 AN: 48

European-Non Finnish (NFE) AF: 0.208 AC: 1249 AN: 6008

Other (OTH) AF: 0.201 AC: 114 AN: 566

GnomAD4 genome AF: 0.209 AC: 31832 AN: 152142 Hom.: 3431 Cov.: 32 AF XY: 0.208 AC XY: 15458 AN XY: 74396

African (AFR) AF: 0.262 AC: 10845 AN: 41466

American (AMR) AF: 0.164 AC: 2507 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3472

East Asian (EAS) AF: 0.178 AC: 925 AN: 5184

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13374 AN: 67994

Other (OTH) AF: 0.190 AC: 402 AN: 2116

Alfa AF: 0.208 Hom.: 569

Bravo AF: 0.207

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs16869658; hg19: chr8-103633762;