dbSNP rs1157: ALCAM:c.*2166G>A (chr3-105576617-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001627.4(ALCAM):c.*2166G>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 0.161 in 152,124 control chromosomes in the GnomAD database, including 2,418 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 0.16 ( 2412 hom., cov: 32)

Exomes 𝑓: 0.21 ( 6 hom. )

Consequence

ALCAM
NM_001627.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11

Publications

23 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001627.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALCAM	NM_001627.4	MANE Select	c.*2166G>A		3_prime_UTR	Exon 16 of 16	NP_001618.2	Q13740-1
	ALCAM	NM_001243280.2		c.*2166G>A		3_prime_UTR	Exon 15 of 15	NP_001230209.1	Q13740-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ALCAM	ENST00000306107.9	TSL:1 MANE Select	c.*2166G>A	3_prime_UTR	Exon 16 of 16	ENSP00000305988.5	Q13740-1
ALCAM	ENST00000472644.6	TSL:1	c.*2166G>A	3_prime_UTR	Exon 15 of 15	ENSP00000419236.2	Q13740-2
ALCAM	ENST00000932235.1		c.*2164G>A	3_prime_UTR	Exon 16 of 16	ENSP00000602294.1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24384

AN:

151682

Hom.:

2410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0425

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.208

AC:

AN:

322

Hom.:

Cov.:

AF XY:

0.173

AC XY:

AN XY:

196

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.198

AC:

AN:

308

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.161

AC:

24376

AN:

151802

Hom.:

2412

Cov.:

AF XY:

0.163

AC XY:

12079

AN XY:

74156

show subpopulations

African (AFR)

AF:

0.0423

AC:

1754

AN:

41452

American (AMR)

AF:

0.208

AC:

3171

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

628

AN:

3470

East Asian (EAS)

AF:

0.165

AC:

853

AN:

5162

South Asian (SAS)

AF:

0.229

AC:

1100

AN:

4810

European-Finnish (FIN)

AF:

0.207

AC:

2170

AN:

10466

Middle Eastern (MID)

AF:

0.182

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.208

AC:

14135

AN:

67896

Other (OTH)

AF:

0.170

AC:

358

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1026

2052

3077

4103

5129

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.186

Hom.:

8058

Bravo

AF:

0.153

Asia WGS

AF:

0.184

AC:

640

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.67

(source)

DANN

Benign

0.68

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over