ENST00000566467.2:n.446+1218T>C

Variant names:

• chr16-55734728-T-C
• rs4580160
• ENST00000566467.2:n.446+1218T>C

Variant summary

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

The ENST00000566467.2(CES1P2):​n.446+1218T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,014 control chromosomes in the GnomAD database, including 27,295 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 0.57 (27295 hom., cov: 32)
• Consequence: CES1P2 ENST00000566467.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 12 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566467.2. 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+1218T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CES1P2	ENST00000566467.2	TSL:6	n.446+1218T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87156 AN: 151896 Hom.: 27273 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.574 AC: 87197 AN: 152014 Hom.: 27295 Cov.: 32 AF XY: 0.570 AC XY: 42376 AN XY: 74284

African (AFR) AF: 0.306 AC: 12692 AN: 41488

American (AMR) AF: 0.683 AC: 10418 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2210 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3006 AN: 5156

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4812

European-Finnish (FIN) AF: 0.661 AC: 6978 AN: 10558

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48017 AN: 67958

Other (OTH) AF: 0.588 AC: 1242 AN: 2112

Alfa AF: 0.654 Hom.: 39096

Bravo AF: 0.566

Asia WGS AF: 0.447 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.52
PhyloP100		-1.6

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: rs4580160;

hg19: chr16-55768640;