rs9928481

Variant names:

• chr16-55734185-A-G
• rs9928481
• ENST00000566467.2:n.446+675A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-55734185-A-G
• chr16-55734185-A-T

Variant summary

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

The NR_033740.1(CES1P2):​n.699+675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,274 control chromosomes in the GnomAD database, including 60,622 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 0.89 (60622 hom., cov: 33)
• Consequence: CES1P2 NR_033740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 1 publications found

Genes affected

CES1P2 (HGNC:48928): (carboxylesterase 1 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_033740.1. 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
	CES1P2	NR_033740.1		n.699+675A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CES1P2	ENST00000566467.2	TSL:6	n.446+675A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135722 AN: 152156 Hom.: 60565 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.892 AC: 135836 AN: 152274 Hom.: 60622 Cov.: 33 AF XY: 0.890 AC XY: 66241 AN XY: 74448

African (AFR) AF: 0.883 AC: 36700 AN: 41548

American (AMR) AF: 0.906 AC: 13865 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3109 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4142 AN: 5184

South Asian (SAS) AF: 0.839 AC: 4051 AN: 4830

European-Finnish (FIN) AF: 0.887 AC: 9396 AN: 10598

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61686 AN: 68024

Other (OTH) AF: 0.883 AC: 1866 AN: 2114

Alfa AF: 0.895 Hom.: 20220

Bravo AF: 0.893

Asia WGS AF: 0.827 AC: 2877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9928481; hg19: chr16-55768097;