Genetic Variant CEACAMP4:n.*141C>G (chr19-43303030-G-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000457676.1(CEACAMP4):n.*141C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 383,960 control chromosomes in the GnomAD database, including 9 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 0.0029 ( 6 hom., cov: 31)

Exomes 𝑓: 0.0025 ( 3 hom. )

Consequence

CEACAMP4
ENST00000457676.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.190

Publications

4 publications found

Variant links:

Genes affected

CEACAMP4 (HGNC:1826): (CEA cell adhesion molecule pseudogene 4)

CEACAMP4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

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

BS2

High Homozygotes in GnomAd4 at 6 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457676.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAMP4	ENST00000457676.1	TSL:6	n.*141C>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.00293

AC:

444

AN:

151774

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000315

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00112

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.0164

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00265

Gnomad OTH

AF:

0.00239

GnomAD4 exome

AF:

0.00251

AC:

583

AN:

232068

Hom.:

AF XY:

0.00248

AC XY:

339

AN XY:

136734

show subpopulations

African (AFR)

AF:

0.000220

AC:

AN:

4544

American (AMR)

AF:

0.00123

AC:

AN:

17010

Ashkenazi Jewish (ASJ)

AF:

0.0122

AC:

AN:

4992

East Asian (EAS)

AF:

0.00

AC:

AN:

7122

South Asian (SAS)

AF:

0.000552

AC:

AN:

41702

European-Finnish (FIN)

AF:

0.0123

AC:

193

AN:

15740

Middle Eastern (MID)

AF:

0.00

AC:

AN:

720

European-Non Finnish (NFE)

AF:

0.00194

AC:

251

AN:

129618

Other (OTH)

AF:

0.00311

AC:

AN:

10620

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

106

132

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00292

AC:

444

AN:

151892

Hom.:

Cov.:

AF XY:

0.00345

AC XY:

256

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.000314

AC:

AN:

41420

American (AMR)

AF:

0.00111

AC:

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0159

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5152

South Asian (SAS)

AF:

0.000208

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.0164

AC:

173

AN:

10542

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00265

AC:

180

AN:

67920

Other (OTH)

AF:

0.00237

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.0000228

Hom.:

25367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

(source)

DANN

Benign

0.60

PhyloP100

-0.19

Splicing

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