Variant rs1805223 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002483.7(CEACAM6):c.126G>A(p.Pro42Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,613,802 control chromosomes in the GnomAD database, including 68,916 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 0.26 ( 5478 hom., cov: 31)

Exomes 𝑓: 0.29 ( 63438 hom. )

Consequence

CEACAM6
NM_002483.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.65

Variant links:

Genes affected

CEACAM6 (HGNC:1818): (CEA cell adhesion molecule 6) This gene encodes a protein that belongs to the carcinoembryonic antigen (CEA) family whose members are glycosyl phosphatidyl inositol (GPI) anchored cell surface glycoproteins. Members of this family play a role in cell adhesion and are widely used as tumor markers in serum immunoassay determinations of carcinoma. This gene affects the sensitivity of tumor cells to adenovirus infection. The protein encoded by this gene acts as a receptor for adherent-invasive E. coli adhesion to the surface of ileal epithelial cells in patients with Crohn's disease. This gene is clustered with genes and pseudogenes of the cell adhesion molecules subgroup of the CEA family on chromosome 19. [provided by RefSeq, Apr 2014]

CEACAM6 links:

ENSG00000267881 (HGNC:):

ENSG00000267881 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP7

Synonymous conserved (PhyloP=-2.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEACAM6	NM_002483.7 linkuse as main transcript	c.126G>A	p.Pro42Pro	synonymous_variant	2/6	ENST00000199764.7	NP_002474.4	P40199
CEACAM6	XM_011526990.3 linkuse as main transcript	c.126G>A	p.Pro42Pro	synonymous_variant	2/5		XP_011525292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CEACAM6	ENST00000199764.7 linkuse as main transcript	c.126G>A	p.Pro42Pro	synonymous_variant	2/6	1	NM_002483.7	ENSP00000199764.6	P40199
ENSG00000267881	ENST00000435837.2 linkuse as main transcript	c.126G>A	p.Pro42Pro	synonymous_variant	2/2	3		ENSP00000469926.1	M0QYM2
CEACAM6	ENST00000595740.1 linkuse as main transcript	c.*26G>A		downstream_gene_variant		4		ENSP00000469752.1	M0QYD3

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39379

AN:

151822

Hom.:

5481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.300

AC:

75499

AN:

251440

Hom.:

11626

AF XY:

0.302

AC XY:

41089

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.334

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.294

Gnomad SAS exome

AF:

0.322

Gnomad FIN exome

AF:

0.337

Gnomad NFE exome

AF:

0.296

Gnomad OTH exome

AF:

0.305

GnomAD4 exome

AF:

0.292

AC:

427155

AN:

1461862

Hom.:

63438

Cov.:

AF XY:

0.293

AC XY:

213226

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.326

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.322

Gnomad4 FIN exome

AF:

0.335

Gnomad4 NFE exome

AF:

0.291

Gnomad4 OTH exome

AF:

0.293

GnomAD4 genome

AF:

0.259

AC:

39399

AN:

151940

Hom.:

5478

Cov.:

AF XY:

0.263

AC XY:

19490

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.277

Gnomad4 ASJ

AF:

0.317

Gnomad4 EAS

AF:

0.279

Gnomad4 SAS

AF:

0.332

Gnomad4 FIN

AF:

0.347

Gnomad4 NFE

AF:

0.294

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.281

Hom.:

2735

Bravo

AF:

0.250

Asia WGS

AF:

0.303

AC:

1054

AN:

3478

EpiCase

AF:

0.296

EpiControl

AF:

0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.9

DANN

Benign

0.53

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over