Genetic Variant CEACAM22P:n.519A>G (chr19-44547413-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 ENST00000446628.5(CEACAM22P):n.519A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,782 control chromosomes in the GnomAD database, including 26,843 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 0.58 ( 26823 hom., cov: 28)

Exomes 𝑓: 0.50 ( 20 hom. )

Consequence

CEACAM22P
ENST00000446628.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.81

Publications

10 publications found

Variant links:

Genes affected

CEACAM22P (HGNC:):

CEACAM22P links:

CEACAM22P (HGNC:38029): (CEA cell adhesion molecule 22, pseudogene)

CEACAM22P 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM22P	NR_027754.2 link	n.519A>G		non_coding_transcript_exon_variant	Exon 3 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CEACAM22P	ENST00000446628.5 link	n.519A>G	non_coding_transcript_exon_variant	Exon 3 of 8	2
CEACAM22P	ENST00000455058.1 link	n.290A>G	non_coding_transcript_exon_variant	Exon 2 of 4	6
CEACAM22P	ENST00000455455.1 link	n.445A>G	non_coding_transcript_exon_variant	Exon 4 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.579

AC:

87696

AN:

151508

Hom.:

26777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.790

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.639

Gnomad SAS

AF:

0.580

Gnomad FIN

AF:

0.464

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.556

GnomAD4 exome

AF:

0.500

AC:

AN:

156

Hom.:

Cov.:

AF XY:

0.482

AC XY:

AN XY:

114

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.667

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

0.917

AC:

AN:

European-Non Finnish (NFE)

AF:

0.426

AC:

AN:

108

Other (OTH)

AF:

0.600

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.579

AC:

87786

AN:

151626

Hom.:

26823

Cov.:

AF XY:

0.575

AC XY:

42603

AN XY:

74038

show subpopulations

African (AFR)

AF:

0.791

AC:

32690

AN:

41338

American (AMR)

AF:

0.523

AC:

7957

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.412

AC:

1428

AN:

3464

East Asian (EAS)

AF:

0.639

AC:

3292

AN:

5148

South Asian (SAS)

AF:

0.579

AC:

2772

AN:

4784

European-Finnish (FIN)

AF:

0.464

AC:

4874

AN:

10506

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.490

AC:

33238

AN:

67878

Other (OTH)

AF:

0.553

AC:

1157

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1734

3467

5201

6934

8668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.562

Hom.:

5865

Bravo

AF:

0.593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.69

(source)

PhyloP100

-2.8

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over