Genetic Variant NM_005581.5:c.714C>T (chr19-44813550-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.714C>T(p.Ala238Ala) 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 (no stars).

Frequency

Genomes: 𝑓 0.073 ( 458 hom., cov: 32)

Exomes 𝑓: 0.067 ( 4230 hom. )

Consequence

BCAM
NM_005581.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

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=-0.76).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-3.37 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.714C>T	p.Ala238Ala	synonymous_variant	Exon 6 of 15	ENST00000270233.12	NP_005572.2	P50895
BCAM	NM_001013257.2 link	c.714C>T	p.Ala238Ala	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.714C>T	p.Ala238Ala	synonymous_variant	Exon 6 of 15	1	NM_005581.5	ENSP00000270233.5		P50895

Frequencies

GnomAD3 genomes

AF:

0.0731

AC:

11125

AN:

152124

Hom.:

457

Cov.:

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.:

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

AF:

0.0731

AC:

11136

AN:

152242

Hom.:

458

Cov.:

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.:

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: no assertion criteria provided

LINK: link

Submissions by phenotype

BCAM-related disorder

Benign:1

Jan 02, 2020

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

-0.76

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.

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