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GeneBe

19-44813547-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005581.5(BCAM):c.711C>T(p.Cys237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 1,612,474 control chromosomes in the GnomAD database, including 4,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.081 ( 543 hom., cov: 32)
Exomes 𝑓: 0.068 ( 4334 hom. )

Consequence

BCAM
NM_005581.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.375
Variant links:
Genes affected
BCAM (HGNC:6722): (basal cell adhesion molecule (Lutheran blood group)) This gene encodes Lutheran blood group glycoprotein, a member of the immunoglobulin superfamily and a receptor for the extracellular matrix protein, laminin. The protein contains five extracellular immunoglobulin domains, a single transmembrane domain, and a short C-terminal cytoplasmic tail. This protein may play a role in epithelial cell cancer and in vaso-occlusion of red blood cells in sickle cell disease. Polymorphisms in this gene define some of the antigens in the Lutheran system and also the Auberger system. Inactivating variants of this gene result in the recessive Lutheran null phenotype, Lu(a-b-), of the Lutheran blood group. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-44813547-C-T is Benign according to our data. Variant chr19-44813547-C-T is described in ClinVar as [Benign]. Clinvar id is 3056456.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.375 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCAMNM_005581.5 linkuse as main transcriptc.711C>T p.Cys237= synonymous_variant 6/15 ENST00000270233.12
BCAMNM_001013257.2 linkuse as main transcriptc.711C>T p.Cys237= synonymous_variant 6/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCAMENST00000270233.12 linkuse as main transcriptc.711C>T p.Cys237= synonymous_variant 6/151 NM_005581.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0810
AC:
12329
AN:
152126
Hom.:
542
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0929
Gnomad AMI
AF:
0.0308
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.0479
Gnomad EAS
AF:
0.0308
Gnomad SAS
AF:
0.178
Gnomad FIN
AF:
0.0753
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0656
Gnomad OTH
AF:
0.0828
GnomAD3 exomes
AF:
0.0862
AC:
21250
AN:
246500
Hom.:
1189
AF XY:
0.0906
AC XY:
12142
AN XY:
134074
show subpopulations
Gnomad AFR exome
AF:
0.0944
Gnomad AMR exome
AF:
0.114
Gnomad ASJ exome
AF:
0.0451
Gnomad EAS exome
AF:
0.0336
Gnomad SAS exome
AF:
0.182
Gnomad FIN exome
AF:
0.0728
Gnomad NFE exome
AF:
0.0653
Gnomad OTH exome
AF:
0.0782
GnomAD4 exome
AF:
0.0681
AC:
99425
AN:
1460230
Hom.:
4334
Cov.:
33
AF XY:
0.0717
AC XY:
52074
AN XY:
726542
show subpopulations
Gnomad4 AFR exome
AF:
0.0946
Gnomad4 AMR exome
AF:
0.116
Gnomad4 ASJ exome
AF:
0.0418
Gnomad4 EAS exome
AF:
0.0320
Gnomad4 SAS exome
AF:
0.178
Gnomad4 FIN exome
AF:
0.0725
Gnomad4 NFE exome
AF:
0.0584
Gnomad4 OTH exome
AF:
0.0709
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0810
AC:
12338
AN:
152244
Hom.:
543
Cov.:
32
AF XY:
0.0843
AC XY:
6279
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0928
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.0479
Gnomad4 EAS
AF:
0.0309
Gnomad4 SAS
AF:
0.178
Gnomad4 FIN
AF:
0.0753
Gnomad4 NFE
AF:
0.0656
Gnomad4 OTH
AF:
0.0819
Alfa
AF:
0.0639
Hom.:
244
Bravo
AF:
0.0800
Asia WGS
AF:
0.117
AC:
407
AN:
3478
EpiCase
AF:
0.0629
EpiControl
AF:
0.0650

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

BCAM-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesDec 23, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
4.5
Dann
Benign
0.85

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: rs3810141; hg19: chr19-45316804; COSMIC: COSV54304151; COSMIC: COSV54304151; API