chr19-44813547-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
NM_005581.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.375
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
?
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 criteria_provided_single_submitter, 1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAM | NM_005581.5 | c.711C>T | p.Cys237= | synonymous_variant | 6/15 | ENST00000270233.12 | |
BCAM | NM_001013257.2 | c.711C>T | p.Cys237= | synonymous_variant | 6/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAM | ENST00000270233.12 | c.711C>T | p.Cys237= | synonymous_variant | 6/15 | 1 | NM_005581.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0810 AC: 12329AN: 152126Hom.: 542 Cov.: 32
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GnomAD3 exomes AF: 0.0862 AC: 21250AN: 246500Hom.: 1189 AF XY: 0.0906 AC XY: 12142AN XY: 134074
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GnomAD4 exome AF: 0.0681 AC: 99425AN: 1460230Hom.: 4334 Cov.: 33 AF XY: 0.0717 AC XY: 52074AN XY: 726542
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GnomAD4 genome ? AF: 0.0810 AC: 12338AN: 152244Hom.: 543 Cov.: 32 AF XY: 0.0843 AC XY: 6279AN XY: 74440
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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 submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 2019 | 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
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BayesDel_noAF
Benign
Cadd
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Dann
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at