rs1157

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ALCAMNM_001627.4 linkuse as main transcriptc.*2166G>A 3_prime_UTR_variant 16/16 ENST00000306107.9 NP_001618.2
ALCAMNM_001243280.2 linkuse as main transcriptc.*2166G>A 3_prime_UTR_variant 15/15 NP_001230209.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ALCAMENST00000306107.9 linkuse as main transcriptc.*2166G>A 3_prime_UTR_variant 16/161 NM_001627.4 ENSP00000305988 A1Q13740-1
ALCAMENST00000472644.6 linkuse as main transcriptc.*2166G>A 3_prime_UTR_variant 15/151 ENSP00000419236 P3Q13740-2

Frequencies

GnomAD3 genomes
AF:
0.161
AC:
24384
AN:
151682
Hom.:
2410
Cov.:
32
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:
67
AN:
322
Hom.:
6
Cov.:
0
AF XY:
0.173
AC XY:
34
AN XY:
196
show subpopulations
Gnomad4 FIN exome
AF:
0.198
Gnomad4 NFE exome
AF:
0.625
Gnomad4 OTH exome
AF:
0.167
GnomAD4 genome
AF:
0.161
AC:
24376
AN:
151802
Hom.:
2412
Cov.:
32
AF XY:
0.163
AC XY:
12079
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.0423
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.181
Gnomad4 EAS
AF:
0.165
Gnomad4 SAS
AF:
0.229
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.208
Gnomad4 OTH
AF:
0.170
Alfa
AF:
0.195
Hom.:
5111
Bravo
AF:
0.153
Asia WGS
AF:
0.184
AC:
640
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.67
DANN
Benign
0.68

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1157; hg19: chr3-105295461; API