dbSNP rs73936843: CEACAM19:c.56-26C>T (chr19-44672570-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001127893.3(CEACAM19):c.56-26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,459,940 control chromosomes in the GnomAD database, including 823 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.043 ( 355 hom., cov: 32)

Exomes 𝑓: 0.0086 ( 468 hom. )

Consequence

CEACAM19
NM_001127893.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.61

Publications

3 publications found

Variant links:

Genes affected

CEACAM19 (HGNC:31951): (CEA cell adhesion molecule 19) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CEACAM19 links:

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

CEACAM16-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

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 2 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001127893.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEACAM19	NM_001127893.3	MANE Select	c.56-26C>T	intron	N/A	NP_001121365.1	Q7Z692-3
CEACAM19	NM_020219.5		c.56-26C>T	intron	N/A	NP_064604.2
CEACAM19	NM_001389722.1		c.56-26C>T	intron	N/A	NP_001376651.1	Q7Z692-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEACAM19	ENST00000358777.10	TSL:1 MANE Select	c.56-26C>T	intron	N/A	ENSP00000351627.4	Q7Z692-3
CEACAM19	ENST00000403660.3	TSL:1	c.56-26C>T	intron	N/A	ENSP00000384887.3	Q7Z692-1
CEACAM19	ENST00000911248.1		c.56-26C>T	intron	N/A	ENSP00000581307.1

Frequencies

GnomAD3 genomes

AF:

0.0430

AC:

6543

AN:

152086

Hom.:

355

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0229

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.0232

Gnomad SAS

AF:

0.0373

Gnomad FIN

AF:

0.0336

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00146

Gnomad OTH

AF:

0.0321

GnomAD2 exomes

AF:

0.0228

AC:

3330

AN:

146092

AF XY:

0.0193

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.0102

Gnomad ASJ exome

AF:

0.0123

Gnomad EAS exome

AF:

0.0134

Gnomad FIN exome

AF:

0.0366

Gnomad NFE exome

AF:

0.00234

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.00864

AC:

11301

AN:

1307736

Hom.:

468

Cov.:

AF XY:

0.00908

AC XY:

5779

AN XY:

636306

show subpopulations

African (AFR)

AF:

0.137

AC:

3861

AN:

28102

American (AMR)

AF:

0.0116

AC:

265

AN:

22856

Ashkenazi Jewish (ASJ)

AF:

0.0129

AC:

244

AN:

18926

East Asian (EAS)

AF:

0.0439

AC:

1533

AN:

34934

South Asian (SAS)

AF:

0.0400

AC:

2380

AN:

59426

European-Finnish (FIN)

AF:

0.0341

AC:

1667

AN:

48936

Middle Eastern (MID)

AF:

0.0105

AC:

AN:

3628

European-Non Finnish (NFE)

AF:

0.000468

AC:

486

AN:

1037452

Other (OTH)

AF:

0.0155

AC:

827

AN:

53476

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

503

1006

1508

2011

2514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

194

388

582

776

970

<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:

0.0431

AC:

6555

AN:

152204

Hom.:

355

Cov.:

AF XY:

0.0435

AC XY:

3239

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.129

AC:

5348

AN:

41496

American (AMR)

AF:

0.0229

AC:

350

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

3472

East Asian (EAS)

AF:

0.0230

AC:

119

AN:

5168

South Asian (SAS)

AF:

0.0369

AC:

178

AN:

4822

European-Finnish (FIN)

AF:

0.0336

AC:

357

AN:

10612

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00146

AC:

AN:

68020

Other (OTH)

AF:

0.0318

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

305

610

916

1221

1526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0251

Hom.:

Bravo

AF:

0.0461

Asia WGS

AF:

0.0360

AC:

127

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

1.6

BranchPoint Hunter

2.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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