3-105457791-G-T

Variant names:

• chr3-105457791-G-T
• rs3910551
• NM_001627.4:c.74-62276G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001627.4(ALCAM):​c.74-62276G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ALCAM NM_001627.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALCAM	NM_001627.4	c.74-62276G>T		intron_variant	Intron 1 of 15	ENST00000306107.9	NP_001618.2
ALCAM	NM_001243280.2	c.74-62276G>T		intron_variant	Intron 1 of 14		NP_001230209.1
ALCAM	NM_001243281.2	c.74-62276G>T		intron_variant	Intron 1 of 13		NP_001230210.1
ALCAM	NM_001243283.2	c.74-62276G>T		intron_variant	Intron 1 of 2		NP_001230212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALCAM	ENST00000306107.9	c.74-62276G>T		intron_variant	Intron 1 of 15	1	NM_001627.4	ENSP00000305988.5
ALCAM	ENST00000472644.6	c.74-62276G>T		intron_variant	Intron 1 of 14	1		ENSP00000419236.2
ALCAM	ENST00000470756.5	n.565-62276G>T		intron_variant	Intron 1 of 2	1
ALCAM	ENST00000481337.5	n.202+16926G>T		intron_variant	Intron 2 of 9	2

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

Alfa AF: 0.00 Hom.: 94

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.5
DANN	Benign	0.82
PhyloP100		0.064

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

Other links and lift over

dbSNP: rs3910551; hg19: chr3-105176635;