3-105457791-G-C

Variant names:

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

Variant summary

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

The NM_001627.4(ALCAM):​c.74-62276G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 152,096 control chromosomes in the GnomAD database, including 1,083 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 0.099 (1083 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALCAM	NM_001627.4	c.74-62276G>C		intron_variant	Intron 1 of 15	ENST00000306107.9	NP_001618.2
ALCAM	NM_001243280.2	c.74-62276G>C		intron_variant	Intron 1 of 14		NP_001230209.1
ALCAM	NM_001243281.2	c.74-62276G>C		intron_variant	Intron 1 of 13		NP_001230210.1
ALCAM	NM_001243283.2	c.74-62276G>C		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>C		intron_variant	Intron 1 of 15	1	NM_001627.4	ENSP00000305988.5
ALCAM	ENST00000472644.6	c.74-62276G>C		intron_variant	Intron 1 of 14	1		ENSP00000419236.2
ALCAM	ENST00000470756.5	n.565-62276G>C		intron_variant	Intron 1 of 2	1
ALCAM	ENST00000481337.5	n.202+16926G>C		intron_variant	Intron 2 of 9	2

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14979 AN: 151980 Hom.: 1080 Cov.: 31

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.0985 AC: 14983 AN: 152096 Hom.: 1083 Cov.: 31 AF XY: 0.104 AC XY: 7758 AN XY: 74352

African (AFR) AF: 0.0203 AC: 842 AN: 41532

American (AMR) AF: 0.188 AC: 2863 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1282 AN: 5150

South Asian (SAS) AF: 0.179 AC: 863 AN: 4822

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10576

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6815 AN: 67972

Other (OTH) AF: 0.127 AC: 268 AN: 2112

Alfa AF: 0.0917 Hom.: 94

Bravo AF: 0.101

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.82
PhyloP100		0.064
Mutation Taster		=99/1	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: rs3910551; hg19: chr3-105176635;