19-44812384-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005581.5(BCAM):c.426C>T(p.Asn142Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000185 in 1,461,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
BCAM
NM_005581.5 synonymous
NM_005581.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.59
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 19-44812384-C-T is Benign according to our data. Variant chr19-44812384-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650085.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.59 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCAM | NM_005581.5 | c.426C>T | p.Asn142Asn | synonymous_variant | 3/15 | ENST00000270233.12 | NP_005572.2 | |
BCAM | NM_001013257.2 | c.426C>T | p.Asn142Asn | synonymous_variant | 3/14 | NP_001013275.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCAM | ENST00000270233.12 | c.426C>T | p.Asn142Asn | synonymous_variant | 3/15 | 1 | NM_005581.5 | ENSP00000270233.5 | ||
BCAM | ENST00000611077.5 | c.426C>T | p.Asn142Asn | synonymous_variant | 3/14 | 5 | ENSP00000481153.1 | |||
BCAM | ENST00000591520.6 | c.363C>T | p.Asn121Asn | synonymous_variant | 3/7 | 3 | ENSP00000467100.2 | |||
BCAM | ENST00000588603.1 | n.421C>T | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249834Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135232
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461690Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727176
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | BCAM: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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