19-44813447-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005581.5(BCAM):c.611T>A(p.Met204Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,610,918 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005581.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAM | NM_005581.5 | c.611T>A | p.Met204Lys | missense_variant | 6/15 | ENST00000270233.12 | |
BCAM | NM_001013257.2 | c.611T>A | p.Met204Lys | missense_variant | 6/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAM | ENST00000270233.12 | c.611T>A | p.Met204Lys | missense_variant | 6/15 | 1 | NM_005581.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00938 AC: 1428AN: 152184Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00949 AC: 2316AN: 244166Hom.: 24 AF XY: 0.00947 AC XY: 1259AN XY: 132956
GnomAD4 exome AF: 0.0103 AC: 14968AN: 1458616Hom.: 130 Cov.: 32 AF XY: 0.0103 AC XY: 7502AN XY: 725620
GnomAD4 genome AF: 0.00937 AC: 1427AN: 152302Hom.: 12 Cov.: 32 AF XY: 0.00935 AC XY: 696AN XY: 74462
ClinVar
Submissions by phenotype
BCAM-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at