Genetic Variant NM_001127893.3: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CEACAM19	NM_001127893.3 link	c.-73C>G	5_prime_UTR_variant	Exon 1 of 8	ENST00000358777.10	NP_001121365.1	Q7Z692-3
CEACAM19	NM_020219.5 link	c.-73C>G	5_prime_UTR_variant	Exon 1 of 8		NP_064604.2	Q7Z692-1
CEACAM19	NM_001389722.1 link	c.-73C>G	5_prime_UTR_variant	Exon 2 of 9		NP_001376651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM19	ENST00000358777.10 link	c.-73C>G		5_prime_UTR_variant	Exon 1 of 8	1	NM_001127893.3	ENSP00000351627.4		Q7Z692-3

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 v4.3

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

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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