19-41709692-CC-GT

Variant names:

• chr19-41709692-CC-GT
• NM_004363.6:c.77_78delCCinsGT
• CEACAM5 p.Thr26Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004363.6(CEACAM5):​c.77_78delCCinsGT​(p.Thr26Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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. T26N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: CEACAM5 NM_004363.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 0 publications found

Genes affected

CEACAM5 (HGNC:1817): (CEA cell adhesion molecule 5) This gene encodes a cell surface glycoprotein that represents the founding member of the carcinoembryonic antigen (CEA) family of proteins. The encoded protein is used as a clinical biomarker for gastrointestinal cancers and may promote tumor development through its role as a cell adhesion molecule. Additionally, the encoded protein may regulate differentiation, apoptosis, and cell polarity. This gene is present in a CEA family gene cluster on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

ENSG00000267881 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004363.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM5	NM_004363.6	MANE Select	c.77_78delCCinsGT	p.Thr26Ser	missense	N/A	NP_004354.3	A0A024R0K5
	CEACAM5	NM_001291484.3		c.77_78delCCinsGT	p.Thr26Ser	missense	N/A	NP_001278413.1	P06731-1
	CEACAM5	NM_001308398.3		c.77_78delCCinsGT	p.Thr26Ser	missense	N/A	NP_001295327.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM5	ENST00000221992.11	TSL:1 MANE Select	c.77_78delCCinsGT	p.Thr26Ser	missense	N/A	ENSP00000221992.5	P06731-1
	CEACAM5	ENST00000405816.5	TSL:1	c.77_78delCCinsGT	p.Thr26Ser	missense	N/A	ENSP00000385072.1	P06731-1
	CEACAM5	ENST00000617332.4	TSL:1	c.77_78delCCinsGT	p.Thr26Ser	missense	N/A	ENSP00000482303.1	P06731-1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-42213611;