dbSNP rs3795018: CEACAM6:c.424+853G>A (chr19-41757812-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.424+853G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,002 control chromosomes in the GnomAD database, including 8,146 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 0.32 ( 8145 hom., cov: 32)

Exomes 𝑓: 0.23 ( 1 hom. )

Consequence

CEACAM6
NM_002483.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.515

Publications

5 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
CEACAM6	NM_002483.7 link	c.424+853G>A	intron_variant	Intron 2 of 5	ENST00000199764.7	NP_002474.4
LOC112268252	XR_002958447.2 link	n.605C>T	non_coding_transcript_exon_variant	Exon 2 of 2
CEACAM6	XM_011526990.3 link	c.424+853G>A	intron_variant	Intron 2 of 4		XP_011525292.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CEACAM6	ENST00000199764.7 link	c.424+853G>A	intron_variant	Intron 2 of 5	1	NM_002483.7	ENSP00000199764.6
ENSG00000268833	ENST00000819471.1 link	n.615C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000268833	ENST00000601409.1 link	n.*86C>T	downstream_gene_variant		4
ENSG00000268833	ENST00000819470.1 link	n.*23C>T	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48947

AN:

151858

Hom.:

8132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.514

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.304

GnomAD4 exome

AF:

0.231

AC:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.231

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.322

AC:

49002

AN:

151976

Hom.:

8145

Cov.:

AF XY:

0.329

AC XY:

24435

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.324

AC:

13423

AN:

41432

American (AMR)

AF:

0.297

AC:

4533

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

1105

AN:

3458

East Asian (EAS)

AF:

0.513

AC:

2648

AN:

5158

South Asian (SAS)

AF:

0.478

AC:

2307

AN:

4822

European-Finnish (FIN)

AF:

0.368

AC:

3888

AN:

10558

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20082

AN:

67950

Other (OTH)

AF:

0.311

AC:

655

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1711

3422

5132

6843

8554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.321

Hom.:

2751

Bravo

AF:

0.316

Asia WGS

AF:

0.501

AC:

1741

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.5

(source)

DANN

Benign

0.75

PhyloP100

0.52

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