Variant 19-44548749-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000446628.5(CEACAM22P):n.498+149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,280 control chromosomes in the GnomAD database, including 1,148 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 0.12 ( 1144 hom., cov: 32)

Exomes 𝑓: 0.21 ( 4 hom. )

Consequence

CEACAM22P
ENST00000446628.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.563

Variant links:

Genes affected

CEACAM22P (HGNC:):

CEACAM22P links:

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

CEACAM22P links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEACAM22P	NR_027754.2 link	n.498+149T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CEACAM22P	ENST00000446628.5 link	n.498+149T>C	intron_variant	2
CEACAM22P	ENST00000455058.1 link	n.269+149T>C	intron_variant	6
CEACAM22P	ENST00000455455.1 link	n.424+149T>C	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18460

AN:

152094

Hom.:

1143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.0949

Gnomad ASJ

AF:

0.0994

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.206

AC:

AN:

Hom.:

AF XY:

0.295

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.121

AC:

18453

AN:

152212

Hom.:

1144

Cov.:

AF XY:

0.123

AC XY:

9123

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.0951

Gnomad4 ASJ

AF:

0.0994

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.125

Hom.:

1379

Bravo

AF:

0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

4.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over