chr2-218661911-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001079866.2(BCS1L):c.613G>A(p.Val205Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,614,120 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001079866.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCS1L | NM_001079866.2 | c.613G>A | p.Val205Ile | missense_variant | Exon 4 of 8 | ENST00000359273.8 | NP_001073335.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00300 AC: 456AN: 152156Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00756 AC: 1900AN: 251326Hom.: 55 AF XY: 0.00562 AC XY: 764AN XY: 135858
GnomAD4 exome AF: 0.00162 AC: 2364AN: 1461846Hom.: 67 Cov.: 33 AF XY: 0.00136 AC XY: 986AN XY: 727222
GnomAD4 genome AF: 0.00297 AC: 452AN: 152274Hom.: 8 Cov.: 32 AF XY: 0.00324 AC XY: 241AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:2
p.Val205Ile in exon 5 of BCS1L: This variant is not expected to have clinical si gnificance because it has been identified in 5.64% (644/11418) of Latino chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs148278887). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
GRACILE syndrome Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
not provided Benign:2
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BCS1L-related disorder Benign:2
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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). -
Mitochondrial complex III deficiency nuclear type 1 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Leigh syndrome Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at