Genetic Variant BCAM:p.Cys237Cys (chr19-44813547-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_005581.5(BCAM):c.711C>T(p.Cys237Cys) 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 (no stars).

Frequency

Genomes: 𝑓 0.081 ( 543 hom., cov: 32)

Exomes 𝑓: 0.068 ( 4334 hom. )

Consequence

BCAM
NM_005581.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

BCAM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.375 with no splicing effect.

BA1

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 rank	MANE	Protein	UniProt
BCAM	NM_005581.5 link	c.711C>T	p.Cys237Cys	synonymous_variant	Exon 6 of 15	ENST00000270233.12	NP_005572.2	P50895
BCAM	NM_001013257.2 link	c.711C>T	p.Cys237Cys	synonymous_variant	Exon 6 of 14		NP_001013275.1	P50895A0A087WXM8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAM	ENST00000270233.12 link	c.711C>T	p.Cys237Cys	synonymous_variant	Exon 6 of 15	1	NM_005581.5	ENSP00000270233.5		P50895

Frequencies

GnomAD3 genomes

AF:

0.0810

AC:

12329

AN:

152126

Hom.:

542

Cov.:

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.:

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

AF:

0.0810

AC:

12338

AN:

152244

Hom.:

543

Cov.:

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: no assertion criteria provided

LINK: link

Submissions by phenotype

BCAM-related disorder

Benign:1

Dec 23, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over