rs16959168

chr19-44521436-T-A

Variant summary

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

The NM_001102597.3(CEACAM20):c.752-684A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,014 control chromosomes in the GnomAD database, including 3,617 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 0.18 (3617 hom., cov: 32)
• Consequence: CEACAM20 NM_001102597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

Genes affected

CEACAM20 (HGNC:24879): (CEA cell adhesion molecule 20) Predicted to be involved in positive regulation of cytokine production. Predicted to act upstream of or within response to bacterium. Predicted to be located in apical plasma membrane and microvillus membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM20	NM_001102597.3	c.752-684A>T		intron_variant		ENST00000614924.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM20	ENST00000614924.5	c.752-684A>T		intron_variant		1	NM_001102597.3	A2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26855 AN: 151894 Hom.: 3609 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.177 AC: 26890 AN: 152014 Hom.: 3617 Cov.: 32 AF XY: 0.176 AC XY: 13080 AN XY: 74328

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0316

Gnomad4 NFE AF: 0.0837

Gnomad4 OTH AF: 0.189

Alfa AF: 0.141 Hom.: 273

Bravo AF: 0.200

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.0
Dann	Benign	0.77

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: rs16959168; hg19: chr19-45025465;