Genetic Variant CEACAM19:c.55+58T>C (chr19-44672044-T-C) – 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.55+58T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,412,662 control chromosomes in the GnomAD database, including 615 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 0.035 ( 234 hom., cov: 32)

Exomes 𝑓: 0.0092 ( 381 hom. )

Consequence

CEACAM19
NM_001127893.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.68

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

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0995 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.55+58T>C	intron	N/A	NP_001121365.1	Q7Z692-3
CEACAM19	NM_020219.5		c.55+58T>C	intron	N/A	NP_064604.2
CEACAM19	NM_001389722.1		c.55+58T>C	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.55+58T>C	intron	N/A	ENSP00000351627.4	Q7Z692-3
CEACAM19	ENST00000403660.3	TSL:1	c.55+58T>C	intron	N/A	ENSP00000384887.3	Q7Z692-1
CEACAM19	ENST00000911248.1		c.55+58T>C	intron	N/A	ENSP00000581307.1

Frequencies

GnomAD3 genomes

AF:

0.0354

AC:

5378

AN:

152034

Hom.:

234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.0231

Gnomad SAS

AF:

0.0377

Gnomad FIN

AF:

0.0337

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00141

Gnomad OTH

AF:

0.0253

GnomAD4 exome

AF:

0.00924

AC:

11641

AN:

1260510

Hom.:

381

AF XY:

0.0101

AC XY:

6375

AN XY:

630196

show subpopulations

African (AFR)

AF:

0.107

AC:

3163

AN:

29444

American (AMR)

AF:

0.0100

AC:

374

AN:

37242

Ashkenazi Jewish (ASJ)

AF:

0.0128

AC:

312

AN:

24290

East Asian (EAS)

AF:

0.0430

AC:

1595

AN:

37054

South Asian (SAS)

AF:

0.0408

AC:

3161

AN:

77448

European-Finnish (FIN)

AF:

0.0341

AC:

1713

AN:

50174

Middle Eastern (MID)

AF:

0.00887

AC:

AN:

4510

European-Non Finnish (NFE)

AF:

0.000502

AC:

475

AN:

946968

Other (OTH)

AF:

0.0151

AC:

808

AN:

53380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

548

1097

1645

2194

2742

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

152

304

456

608

760

<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:

0.0354

AC:

5383

AN:

152152

Hom.:

234

Cov.:

AF XY:

0.0365

AC XY:

2714

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.102

AC:

4233

AN:

41490

American (AMR)

AF:

0.0202

AC:

308

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

3466

East Asian (EAS)

AF:

0.0230

AC:

119

AN:

5172

South Asian (SAS)

AF:

0.0373

AC:

180

AN:

4824

European-Finnish (FIN)

AF:

0.0337

AC:

357

AN:

10602

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00141

AC:

AN:

67996

Other (OTH)

AF:

0.0251

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

247

495

742

990

1237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

168

224

280

<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:

0.0131

Hom.:

Bravo

AF:

0.0373

Asia WGS

AF:

0.0350

AC:

123

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.26

(source)

DANN

Benign

0.60

PhyloP100

-1.7

PromoterAI

0.014

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over