16-55853372-G-T

Position:

• chr16-55853372-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001143685.2(CES5A):​c.1126-344C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,088 control chromosomes in the GnomAD database, including 37,871 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 0.70 (37871 hom., cov: 33)
• Consequence: CES5A NM_001143685.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

CES5A (HGNC:26459): (carboxylesterase 5A) This gene encodes a member of the carboxylesterase large family. The family members are responsible for the hydrolysis or transesterification of various xenobiotics, such as cocaine and heroin, and endogenous substrates with ester, thioester, or amide bonds. They also participate in fatty acyl and cholesterol ester metabolism, and may play a role in the blood-brain barrier system. This gene, also called CES5, is predominantly expressed in peripheral tissues, including brain, kidney, lung and testis. It encodes a secreted enzyme. Because of high levels in the urine of male domestic cats, this enzyme is also called cauxin (carboxylesterase-like urinary excreted protein). The enzyme functions in regulating the production of a pheromone precursor and may contribute to lipid and cholesterol transfer processes within male reproductive fluids. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

CES5A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CES5A	NM_001143685.2	c.1126-344C>A		intron_variant		ENST00000290567.14	NP_001137157.1
CES5A	NM_001190158.1	c.1213-344C>A		intron_variant			NP_001177087.1
CES5A	NM_145024.3	c.1126-344C>A		intron_variant			NP_659461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CES5A	ENST00000290567.14	c.1126-344C>A		intron_variant		1	NM_001143685.2	ENSP00000290567.9

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107064 AN: 151970 Hom.: 37845 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.705 AC: 107151 AN: 152088 Hom.: 37871 Cov.: 33 AF XY: 0.705 AC XY: 52426 AN XY: 74362

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.708

Alfa AF: 0.724 Hom.: 6762

Bravo AF: 0.707

Asia WGS AF: 0.686 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1819829; hg19: chr16-55887284;