dbSNP rs2165538: CEACAM19:c.-73C>G (chr19-44671859-C-G) – 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.-73C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 1,396,470 control chromosomes in the GnomAD database, including 1,456 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 0.058 ( 723 hom., cov: 32)

Exomes 𝑓: 0.011 ( 733 hom. )

Consequence

CEACAM19
NM_001127893.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118

Publications

2 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=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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
CEACAM19	NM_001127893.3	MANE Select	c.-73C>G	5_prime_UTR	Exon 1 of 8	NP_001121365.1
CEACAM19	NM_020219.5		c.-73C>G	5_prime_UTR	Exon 1 of 8	NP_064604.2
CEACAM19	NM_001389722.1		c.-73C>G	5_prime_UTR	Exon 2 of 9	NP_001376651.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CEACAM19	ENST00000358777.10	TSL:1 MANE Select	c.-73C>G	5_prime_UTR	Exon 1 of 8	ENSP00000351627.4
CEACAM19	ENST00000403660.3	TSL:1	c.-73C>G	5_prime_UTR	Exon 1 of 8	ENSP00000384887.3
CEACAM19	ENST00000911248.1		c.-73C>G	5_prime_UTR	Exon 2 of 10	ENSP00000581307.1

Frequencies

GnomAD3 genomes

AF:

0.0578

AC:

8789

AN:

152116

Hom.:

722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0263

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.0226

Gnomad SAS

AF:

0.0383

Gnomad FIN

AF:

0.0335

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00157

Gnomad OTH

AF:

0.0459

GnomAD4 exome

AF:

0.0114

AC:

14187

AN:

1244236

Hom.:

733

Cov.:

AF XY:

0.0120

AC XY:

7453

AN XY:

622220

show subpopulations

African (AFR)

AF:

0.189

AC:

5399

AN:

28628

American (AMR)

AF:

0.0145

AC:

519

AN:

35840

Ashkenazi Jewish (ASJ)

AF:

0.0126

AC:

305

AN:

24180

East Asian (EAS)

AF:

0.0443

AC:

1576

AN:

35590

South Asian (SAS)

AF:

0.0408

AC:

3126

AN:

76542

European-Finnish (FIN)

AF:

0.0342

AC:

1674

AN:

48968

Middle Eastern (MID)

AF:

0.0116

AC:

AN:

3784

European-Non Finnish (NFE)

AF:

0.000547

AC:

513

AN:

937944

Other (OTH)

AF:

0.0195

AC:

1031

AN:

52760

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

676

1353

2029

2706

3382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

212

424

636

848

1060

<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:

0.0578

AC:

8799

AN:

152234

Hom.:

723

Cov.:

AF XY:

0.0579

AC XY:

4309

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.181

AC:

7502

AN:

41516

American (AMR)

AF:

0.0262

AC:

401

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

3468

East Asian (EAS)

AF:

0.0224

AC:

116

AN:

5174

South Asian (SAS)

AF:

0.0379

AC:

183

AN:

4830

European-Finnish (FIN)

AF:

0.0335

AC:

356

AN:

10620

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00157

AC:

107

AN:

68012

Other (OTH)

AF:

0.0454

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

374

747

1121

1494

1868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0352

Hom.:

Bravo

AF:

0.0624

Asia WGS

AF:

0.0390

AC:

137

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.2

(source)

DANN

Benign

0.84

PhyloP100

-0.12

PromoterAI

-0.015

Neutral

(source)

Mutation Taster

=300/0

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

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