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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
CEACAM19	NM_001127893.3 link	c.55+58T>C	intron_variant	Intron 1 of 7	ENST00000358777.10	NP_001121365.1
CEACAM19	NM_020219.5 link	c.55+58T>C	intron_variant	Intron 1 of 7		NP_064604.2
CEACAM19	NM_001389722.1 link	c.55+58T>C	intron_variant	Intron 2 of 8		NP_001376651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM19	ENST00000358777.10 link	c.55+58T>C		intron_variant	Intron 1 of 7	1	NM_001127893.3	ENSP00000351627.4

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over