rs11559013

Positions:

• chr3-105575658-G-A
• chr3-105575658-G-C
• chr3-105575658-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001627.4(ALCAM):​c.*1207G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,342 control chromosomes in the GnomAD database, including 827 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 0.087 (826 hom., cov: 32)
  • Exomes 𝑓: 0.080 (1 hom.)
• Consequence: ALCAM NM_001627.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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]

ALCAM (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALCAM	NM_001627.4	c.*1207G>A		3_prime_UTR_variant	16/16	ENST00000306107.9	NP_001618.2
ALCAM	NM_001243280.2	c.*1207G>A		3_prime_UTR_variant	15/15		NP_001230209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALCAM	ENST00000306107.9	c.*1207G>A		3_prime_UTR_variant	16/16	1	NM_001627.4	ENSP00000305988.5
ALCAM	ENST00000472644.6	c.*1207G>A		3_prime_UTR_variant	15/15	1		ENSP00000419236.2
ALCAM	ENST00000465413.6	c.*1207G>A		3_prime_UTR_variant	10/10	2		ENSP00000418937.2
ALCAM	ENST00000491388.6	n.2589G>A		non_coding_transcript_exon_variant	8/8	2

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13268 AN: 151814 Hom.: 826 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0335

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0825

GnomAD4 exome AF: 0.0805 AC: 33 AN: 410 Hom.: 1 Cov.: 0 AF XY: 0.0703 AC XY: 18 AN XY: 256

Gnomad4 FIN exome AF: 0.0817

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0873 AC: 13269 AN: 151932 Hom.: 826 Cov.: 32 AF XY: 0.0891 AC XY: 6616 AN XY: 74244

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0392

Gnomad4 ASJ AF: 0.0335

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0426

Gnomad4 OTH AF: 0.0817

Alfa AF: 0.0474 Hom.: 171

Bravo AF: 0.0879

Asia WGS AF: 0.0880 AC: 306 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs11559013; hg19: chr3-105294502;