chr19-42527217-G-A

Variant names:

Variant summary

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

The NM_001712.5(CEACAM1):c.248C>T(p.Ala83Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 1,613,440 control chromosomes in the GnomAD database, including 2,573 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A83T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.094 ( 1439 hom., cov: 32)

Exomes 𝑓: 0.011 ( 1134 hom. )

Consequence

CEACAM1
NM_001712.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.28

Publications

17 publications found

Variant links:

Genes affected

CEACAM1 (HGNC:1814): (CEA cell adhesion molecule 1) This gene encodes a member of the carcinoembryonic antigen (CEA) gene family, which belongs to the immunoglobulin superfamily. Two subgroups of the CEA family, the CEA cell adhesion molecules and the pregnancy-specific glycoproteins, are located within a 1.2 Mb cluster on the long arm of chromosome 19. Eleven pseudogenes of the CEA cell adhesion molecule subgroup are also found in the cluster. The encoded protein was originally described in bile ducts of liver as biliary glycoprotein. Subsequently, it was found to be a cell-cell adhesion molecule detected on leukocytes, epithelia, and endothelia. The encoded protein mediates cell adhesion via homophilic as well as heterophilic binding to other proteins of the subgroup. Multiple cellular activities have been attributed to the encoded protein, including roles in the differentiation and arrangement of tissue three-dimensional structure, angiogenesis, apoptosis, tumor suppression, metastasis, and the modulation of innate and adaptive immune responses. Multiple transcript variants encoding different isoforms have been reported, but the full-length nature of all variants has not been defined. [provided by RefSeq, May 2010]

CEACAM1 links:

LIPE-AS1 (HGNC:48589): (LIPE antisense RNA 1)

LIPE-AS1 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 (MetaRNN=0.0027994514).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001712.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CEACAM1	NM_001712.5	MANE Select	c.248C>T	p.Ala83Val	missense	Exon 2 of 9	NP_001703.2
CEACAM1	NM_001205344.2		c.248C>T	p.Ala83Val	missense	Exon 2 of 8	NP_001192273.1
CEACAM1	NM_001024912.3		c.248C>T	p.Ala83Val	missense	Exon 2 of 8	NP_001020083.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CEACAM1	ENST00000161559.11	TSL:1 MANE Select	c.248C>T	p.Ala83Val	missense	Exon 2 of 9	ENSP00000161559.6
CEACAM1	ENST00000403444.7	TSL:1	c.248C>T	p.Ala83Val	missense	Exon 2 of 8	ENSP00000384709.3
CEACAM1	ENST00000358394.7	TSL:1	c.248C>T	p.Ala83Val	missense	Exon 2 of 9	ENSP00000351165.2

Frequencies

GnomAD3 genomes

AF:

0.0936

AC:

14188

AN:

151598

Hom.:

1428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0443

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.000772

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.00193

Gnomad OTH

AF:

0.0777

GnomAD2 exomes

AF:

0.0248

AC:

6228

AN:

251360

AF XY:

0.0182

show subpopulations

Gnomad AFR exome

AF:

0.318

Gnomad AMR exome

AF:

0.0196

Gnomad ASJ exome

AF:

0.00506

Gnomad EAS exome

AF:

0.000326

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00200

Gnomad OTH exome

AF:

0.0158

GnomAD4 exome

AF:

0.0106

AC:

15477

AN:

1461726

Hom.:

1134

Cov.:

AF XY:

0.00939

AC XY:

6829

AN XY:

727174

show subpopulations

African (AFR)

AF:

0.332

AC:

11087

AN:

33346

American (AMR)

AF:

0.0214

AC:

957

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00455

AC:

119

AN:

26136

East Asian (EAS)

AF:

0.000327

AC:

AN:

39700

South Asian (SAS)

AF:

0.000974

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.0000187

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.0321

AC:

185

AN:

5768

European-Non Finnish (NFE)

AF:

0.00131

AC:

1455

AN:

1111988

Other (OTH)

AF:

0.0261

AC:

1576

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

577

1154

1732

2309

2886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

360

720

1080

1440

1800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0939

AC:

14249

AN:

151714

Hom.:

1439

Cov.:

AF XY:

0.0901

AC XY:

6686

AN XY:

74168

show subpopulations

African (AFR)

AF:

0.322

AC:

13229

AN:

41108

American (AMR)

AF:

0.0442

AC:

674

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.00605

AC:

AN:

3470

East Asian (EAS)

AF:

0.000774

AC:

AN:

5166

South Asian (SAS)

AF:

0.00166

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10598

Middle Eastern (MID)

AF:

0.0274

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00193

AC:

131

AN:

67986

Other (OTH)

AF:

0.0826

AC:

174

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

411

823

1234

1646

2057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.0287

Hom.:

130

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.308

AC:

1359

ESP6500EA

AF:

0.00256

AC:

ExAC

AF:

0.0297

AC:

3612

Asia WGS

AF:

0.0510

AC:

176

AN:

3478

EpiCase

AF:

0.00234

EpiControl

AF:

0.00284

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.0040

(source)

DANN

Benign

0.55

DEOGEN2

Benign

0.064

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.0067

LIST_S2

Benign

0.054

MetaRNN

Benign

0.0028

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.3

PhyloP100

-4.3

PrimateAI

Benign

0.25

PROVEAN

Benign

2.3

REVEL

Benign

0.072

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0010

Vest4

0.031

MPC

0.17

ClinPred

0.0026

GERP RS

-6.2

Varity_R

0.13

gMVP

0.098

Mutation Taster

=99/1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over