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GeneBe

19-44813550-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.714C>T(p.Ala238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 1,612,542 control chromosomes in the GnomAD database, including 4,688 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.073 ( 458 hom., cov: 32)
Exomes 𝑓: 0.067 ( 4230 hom. )

Consequence

BCAM
NM_005581.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.37
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=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-44813550-C-T is Benign according to our data. Variant chr19-44813550-C-T is described in ClinVar as [Benign]. Clinvar id is 3056244.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=-3.37 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.714C>T p.Ala238= synonymous_variant 6/15 ENST00000270233.12
BCAMNM_001013257.2 linkuse as main transcriptc.714C>T p.Ala238= synonymous_variant 6/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCAMENST00000270233.12 linkuse as main transcriptc.714C>T p.Ala238= synonymous_variant 6/151 NM_005581.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0731
AC:
11125
AN:
152124
Hom.:
457
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0657
Gnomad AMI
AF:
0.0308
Gnomad AMR
AF:
0.115
Gnomad ASJ
AF:
0.0479
Gnomad EAS
AF:
0.0308
Gnomad SAS
AF:
0.178
Gnomad FIN
AF:
0.0754
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0655
Gnomad OTH
AF:
0.0757
GnomAD3 exomes
AF:
0.0842
AC:
20770
AN:
246704
Hom.:
1147
AF XY:
0.0892
AC XY:
11964
AN XY:
134170
show subpopulations
Gnomad AFR exome
AF:
0.0677
Gnomad AMR exome
AF:
0.113
Gnomad ASJ exome
AF:
0.0450
Gnomad EAS exome
AF:
0.0337
Gnomad SAS exome
AF:
0.182
Gnomad FIN exome
AF:
0.0723
Gnomad NFE exome
AF:
0.0651
Gnomad OTH exome
AF:
0.0771
GnomAD4 exome
AF:
0.0672
AC:
98167
AN:
1460300
Hom.:
4230
Cov.:
33
AF XY:
0.0710
AC XY:
51582
AN XY:
726562
show subpopulations
Gnomad4 AFR exome
AF:
0.0643
Gnomad4 AMR exome
AF:
0.114
Gnomad4 ASJ exome
AF:
0.0418
Gnomad4 EAS exome
AF:
0.0319
Gnomad4 SAS exome
AF:
0.178
Gnomad4 FIN exome
AF:
0.0725
Gnomad4 NFE exome
AF:
0.0583
Gnomad4 OTH exome
AF:
0.0693
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0731
AC:
11136
AN:
152242
Hom.:
458
Cov.:
32
AF XY:
0.0767
AC XY:
5708
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.0658
Gnomad4 AMR
AF:
0.115
Gnomad4 ASJ
AF:
0.0479
Gnomad4 EAS
AF:
0.0309
Gnomad4 SAS
AF:
0.178
Gnomad4 FIN
AF:
0.0754
Gnomad4 NFE
AF:
0.0655
Gnomad4 OTH
AF:
0.0749
Alfa
AF:
0.0528
Hom.:
86
Bravo
AF:
0.0714
Asia WGS
AF:
0.116
AC:
402
AN:
3478
EpiCase
AF:
0.0628
EpiControl
AF:
0.0648

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 SciencesJan 02, 2020This 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
-0.76
Cadd
Benign
0.25
Dann
Benign
0.81

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: rs3810140; hg19: chr19-45316807; COSMIC: COSV54302950; COSMIC: COSV54302950; API