rs16959168

Variant names:

• chr19-44521436-T-A
• rs16959168
• NM_001102597.3:c.752-684A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CEACAM20	NM_001102597.3	c.752-684A>T		intron_variant	Intron 4 of 11	ENST00000614924.5	NP_001096067.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM20	ENST00000614924.5	c.752-684A>T		intron_variant	Intron 4 of 11	1	NM_001102597.3	ENSP00000481937.1

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

African (AFR) AF: 0.355 AC: 14730 AN: 41438

American (AMR) AF: 0.228 AC: 3473 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3468

East Asian (EAS) AF: 0.147 AC: 761 AN: 5164

South Asian (SAS) AF: 0.166 AC: 801 AN: 4826

European-Finnish (FIN) AF: 0.0316 AC: 336 AN: 10624

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0837 AC: 5683 AN: 67920

Other (OTH) AF: 0.189 AC: 399 AN: 2110

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
PhyloP100		0.34

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

Other links and lift over

dbSNP: rs16959168; hg19: chr19-45025465;