chr19-41579536-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001098506.4(CEACAM21):​c.608C>T​(p.Pro203Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P203H) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

CEACAM21
NM_001098506.4 missense

Scores

1
4
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.853
Variant links:
Genes affected
CEACAM21 (HGNC:28834): (CEA cell adhesion molecule 21) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29060012).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEACAM21NM_001098506.4 linkc.608C>T p.Pro203Leu missense_variant Exon 3 of 7 ENST00000401445.4 NP_001091976.3 Q3KPI0-1A0A0G2JSC8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEACAM21ENST00000401445.4 linkc.608C>T p.Pro203Leu missense_variant Exon 3 of 7 1 NM_001098506.4 ENSP00000385739.2 Q3KPI0-1
CEACAM21ENST00000457737.5 linkn.*115C>T non_coding_transcript_exon_variant Exon 3 of 7 1 ENSP00000390697.1 Q3KPI0-3
CEACAM21ENST00000457737.5 linkn.*115C>T 3_prime_UTR_variant Exon 3 of 7 1 ENSP00000390697.1 Q3KPI0-3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1460612
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
726486
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.44
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
3.9
DANN
Uncertain
0.98
Eigen
Benign
-0.49
Eigen_PC
Benign
-0.77
FATHMM_MKL
Benign
0.0059
N
M_CAP
Benign
0.0018
T
MetaRNN
Benign
0.29
T;T;T
MetaSVM
Benign
-1.0
T
PROVEAN
Pathogenic
-9.5
D;D;D
REVEL
Benign
0.047
Sift
Uncertain
0.0010
D;D;D
Sift4G
Uncertain
0.021
D;T;T
Vest4
0.18
MutPred
0.48
.;Loss of disorder (P = 0.0736);Loss of disorder (P = 0.0736);
MVP
0.14
MPC
0.057
ClinPred
0.94
D
GERP RS
-1.8
gMVP
0.12

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-42085889; API