rs150607806

Variant names:

• chr3-105524360-T-C
• rs150607806
• NM_001627.4:c.246T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-105524360-T-C
• chr3-105524360-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001627.4(ALCAM):​c.246T>C​(p.Asp82Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,614,128 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0017 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0020 (4 hom.)
• Consequence: ALCAM NM_001627.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.454
• 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant 3-105524360-T-C is Benign according to our data. Variant chr3-105524360-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3904826.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALCAM	NM_001627.4	c.246T>C	p.Asp82Asp	synonymous_variant	Exon 3 of 16	ENST00000306107.9	NP_001618.2
ALCAM	NM_001243280.2	c.246T>C	p.Asp82Asp	synonymous_variant	Exon 3 of 15		NP_001230209.1
ALCAM	NM_001243281.2	c.246T>C	p.Asp82Asp	synonymous_variant	Exon 3 of 14		NP_001230210.1
ALCAM	NM_001243283.2	c.246T>C	p.Asp82Asp	synonymous_variant	Exon 3 of 3		NP_001230212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALCAM	ENST00000306107.9	c.246T>C	p.Asp82Asp	synonymous_variant	Exon 3 of 16	1	NM_001627.4	ENSP00000305988.5

Frequencies

GnomAD3 genomes AF: 0.00166 AC: 252 AN: 152172 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000531

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00242

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00256

Gnomad OTH AF: 0.00430

GnomAD2 exomes AF: 0.00174 AC: 437 AN: 251446 AF XY: 0.00173

Gnomad AFR exome AF: 0.000492

Gnomad AMR exome AF: 0.00228

Gnomad ASJ exome AF: 0.00218

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000924

Gnomad NFE exome AF: 0.00229

Gnomad OTH exome AF: 0.00228

GnomAD4 exome AF: 0.00204 AC: 2977 AN: 1461838 Hom.: 4 Cov.: 31 AF XY: 0.00204 AC XY: 1482 AN XY: 727214

African (AFR) AF: 0.000209 AC: 7 AN: 33480

American (AMR) AF: 0.00233 AC: 104 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00168 AC: 44 AN: 26130

East Asian (EAS) AF: 0.00 AC: 0 AN: 39692

South Asian (SAS) AF: 0.00152 AC: 131 AN: 86256

European-Finnish (FIN) AF: 0.0000936 AC: 5 AN: 53420

Middle Eastern (MID) AF: 0.00104 AC: 6 AN: 5768

European-Non Finnish (NFE) AF: 0.00231 AC: 2572 AN: 1111974

Other (OTH) AF: 0.00179 AC: 108 AN: 60394

GnomAD4 genome AF: 0.00165 AC: 252 AN: 152290 Hom.: 0 Cov.: 32 AF XY: 0.00140 AC XY: 104 AN XY: 74476

African (AFR) AF: 0.000529 AC: 22 AN: 41564

American (AMR) AF: 0.00242 AC: 37 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4824

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00256 AC: 174 AN: 67994

Other (OTH) AF: 0.00426 AC: 9 AN: 2114

Alfa AF: 0.00151 Hom.: 0

Bravo AF: 0.00165

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.00196

EpiControl AF: 0.00213

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ALCAM: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	5.7
DANN	Benign	0.49
PhyloP100		0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=96/4	polymorphism

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: rs150607806; hg19: chr3-105243204;