3-105541676-CG-AA

Variant names:

• chr3-105541676-CG-AA
• NM_001627.4:c.902_903delCGinsAA
• ALCAM p.Thr301Lys

Variant summary

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

The NM_001627.4(ALCAM):​c.902_903delCGinsAA​(p.Thr301Lys) 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. T301M) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ALCAM NM_001627.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.86
• Publications: 0 publications found

Genes affected

ALCAM (HGNC:400): (activated leukocyte cell adhesion molecule) This gene encodes activated leukocyte cell adhesion molecule (ALCAM), also known as CD166 (cluster of differentiation 166), which is a member of a subfamily of immunoglobulin receptors with five immunoglobulin-like domains (VVC2C2C2) in the extracellular domain. This protein binds to T-cell differentiation antigene CD6, and is implicated in the processes of cell adhesion and migration. Multiple alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, Aug 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001627.4. 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
	ALCAM	NM_001627.4	MANE Select	c.902_903delCGinsAA	p.Thr301Lys	missense	N/A	NP_001618.2	Q13740-1
	ALCAM	NM_001243280.2		c.902_903delCGinsAA	p.Thr301Lys	missense	N/A	NP_001230209.1	Q13740-2
	ALCAM	NM_001243281.2		c.902_903delCGinsAA	p.Thr301Lys	missense	N/A	NP_001230210.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALCAM	ENST00000306107.9	TSL:1 MANE Select	c.902_903delCGinsAA	p.Thr301Lys	missense	N/A	ENSP00000305988.5	Q13740-1
	ALCAM	ENST00000472644.6	TSL:1	c.902_903delCGinsAA	p.Thr301Lys	missense	N/A	ENSP00000419236.2	Q13740-2
	ALCAM	ENST00000880066.1		c.968_969delCGinsAA	p.Thr323Lys	missense	N/A	ENSP00000550125.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

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: chr3-105260520;