dbSNP rs11559013: ALCAM:c.*1207G>A (chr3-105575658-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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16

Publications

11 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=-0.57).

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 rank	MANE	Protein	UniProt
ALCAM	NM_001627.4 link	c.*1207G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000306107.9	NP_001618.2
ALCAM	NM_001243280.2 link	c.*1207G>A		3_prime_UTR_variant	Exon 15 of 15		NP_001230209.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ALCAM	ENST00000306107.9 link	c.*1207G>A	3_prime_UTR_variant	Exon 16 of 16	1	NM_001627.4	ENSP00000305988.5
ALCAM	ENST00000472644.6 link	c.*1207G>A	3_prime_UTR_variant	Exon 15 of 15	1		ENSP00000419236.2
ALCAM	ENST00000491388.6 link	n.2589G>A	non_coding_transcript_exon_variant	Exon 8 of 8	2
ALCAM	ENST00000465413.6 link	c.*1207G>A	3_prime_UTR_variant	Exon 10 of 10	2		ENSP00000418937.2

Frequencies

GnomAD3 genomes

AF:

0.0874

AC:

13268

AN:

151814

Hom.:

826

Cov.:

show subpopulations

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:

AN:

410

Hom.:

Cov.:

AF XY:

0.0703

AC XY:

AN XY:

256

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:

0.0817

AC:

AN:

404

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0873

AC:

13269

AN:

151932

Hom.:

826

Cov.:

AF XY:

0.0891

AC XY:

6616

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.178

AC:

7371

AN:

41418

American (AMR)

AF:

0.0392

AC:

598

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.0335

AC:

116

AN:

3464

East Asian (EAS)

AF:

0.118

AC:

607

AN:

5154

South Asian (SAS)

AF:

0.0847

AC:

408

AN:

4816

European-Finnish (FIN)

AF:

0.103

AC:

1083

AN:

10534

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0426

AC:

2897

AN:

67982

Other (OTH)

AF:

0.0817

AC:

172

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

591

1182

1772

2363

2954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.0502

Hom.:

252

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

(source)

DANN

Benign

0.46

PhyloP100

1.2

Mutation Taster

=99/1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over