Genetic Variant CEACAM6:c.425-508G>A (chr19-41760741-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002483.7(CEACAM6):c.425-508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,082 control chromosomes in the GnomAD database, including 22,467 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 0.51 ( 22467 hom., cov: 32)

Consequence

CEACAM6
NM_002483.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.629

Publications

9 publications found

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 Gene-Disease associations (from GenCC):

cystic fibrosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CEACAM6 links:

ENSG00000268833 (HGNC:):

ENSG00000268833 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM6	NM_002483.7 link	c.425-508G>A		intron_variant	Intron 2 of 5	ENST00000199764.7	NP_002474.4	P40199
CEACAM6	XM_011526990.3 link	c.425-508G>A		intron_variant	Intron 2 of 4		XP_011525292.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEACAM6	ENST00000199764.7 link	c.425-508G>A	intron_variant	Intron 2 of 5	1	NM_002483.7	ENSP00000199764.6	P40199
ENSG00000268833	ENST00000601409.1 link	n.384-2660C>T	intron_variant	Intron 1 of 1	4
ENSG00000268833	ENST00000819470.1 link	n.111-2660C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77878

AN:

151964

Hom.:

22407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.786

Gnomad AMI

AF:

0.304

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.467

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

GnomAD4 genome

AF:

0.513

AC:

77998

AN:

152082

Hom.:

22467

Cov.:

AF XY:

0.511

AC XY:

37990

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.786

AC:

32629

AN:

41500

American (AMR)

AF:

0.492

AC:

7522

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1241

AN:

3464

East Asian (EAS)

AF:

0.591

AC:

3054

AN:

5164

South Asian (SAS)

AF:

0.407

AC:

1958

AN:

4816

European-Finnish (FIN)

AF:

0.385

AC:

4064

AN:

10568

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.385

AC:

26174

AN:

67974

Other (OTH)

AF:

0.470

AC:

991

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1711

3423

5134

6846

8557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.408

Hom.:

20334

Bravo

AF:

0.537

Asia WGS

AF:

0.488

AC:

1695

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.79

(source)

DANN

Benign

0.29

PhyloP100

-0.63

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over