3-105367241-C-T

Variant names:

• chr3-105367241-C-T
• rs6437585
• ENST00000470756.5:n.324C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000470756.5(ALCAM):​n.324C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0919 in 623,554 control chromosomes in the GnomAD database, including 3,010 homozygotes. 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: 𝑓 0.097 (791 hom., cov: 31)
  • Exomes 𝑓: 0.090 (2219 hom.)
• Consequence: ALCAM ENST00000470756.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 17 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALCAM	NM_001627.4	c.-168C>T		5_prime_UTR_variant	Exon 1 of 16	ENST00000306107.9	NP_001618.2
ALCAM	NM_001243280.2	c.-168C>T		5_prime_UTR_variant	Exon 1 of 15		NP_001230209.1
ALCAM	NM_001243281.2	c.-168C>T		5_prime_UTR_variant	Exon 1 of 14		NP_001230210.1
ALCAM	NM_001243283.2	c.-168C>T		5_prime_UTR_variant	Exon 1 of 3		NP_001230212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALCAM	ENST00000470756.5	n.324C>T		non_coding_transcript_exon_variant	Exon 1 of 3	1
ALCAM	ENST00000306107.9	c.-168C>T		5_prime_UTR_variant	Exon 1 of 16	1	NM_001627.4	ENSP00000305988.5
ALCAM	ENST00000472644.6	c.-168C>T		upstream_gene_variant		1		ENSP00000419236.2

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14749 AN: 151790 Hom.: 788 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0855

GnomAD4 exome AF: 0.0903 AC: 42577 AN: 471646 Hom.: 2219 Cov.: 6 AF XY: 0.0930 AC XY: 23054 AN XY: 247794

African (AFR) AF: 0.135 AC: 1644 AN: 12164

American (AMR) AF: 0.0520 AC: 943 AN: 18136

Ashkenazi Jewish (ASJ) AF: 0.0574 AC: 755 AN: 13150

East Asian (EAS) AF: 0.141 AC: 4151 AN: 29418

South Asian (SAS) AF: 0.156 AC: 7219 AN: 46418

European-Finnish (FIN) AF: 0.124 AC: 4704 AN: 37876

Middle Eastern (MID) AF: 0.0826 AC: 163 AN: 1974

European-Non Finnish (NFE) AF: 0.0726 AC: 20800 AN: 286676

Other (OTH) AF: 0.0851 AC: 2198 AN: 25834

GnomAD4 genome AF: 0.0971 AC: 14754 AN: 151908 Hom.: 791 Cov.: 31 AF XY: 0.0989 AC XY: 7341 AN XY: 74224

African (AFR) AF: 0.137 AC: 5665 AN: 41430

American (AMR) AF: 0.0565 AC: 864 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3468

East Asian (EAS) AF: 0.127 AC: 645 AN: 5088

South Asian (SAS) AF: 0.154 AC: 741 AN: 4810

European-Finnish (FIN) AF: 0.131 AC: 1384 AN: 10548

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5012 AN: 67966

Other (OTH) AF: 0.0846 AC: 178 AN: 2104

Alfa AF: 0.0789 Hom.: 509

Bravo AF: 0.0945

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.93
PhyloP100		-0.35
PromoterAI		-0.024	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	polymorphism (auto)

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: rs6437585; hg19: chr3-105086085;