rs75240042
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015340.4(LARS2):c.235-12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,611,100 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015340.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 230AN: 152140Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000593 AC: 148AN: 249520Hom.: 0 AF XY: 0.000467 AC XY: 63AN XY: 134910
GnomAD4 exome AF: 0.000242 AC: 353AN: 1458842Hom.: 2 Cov.: 30 AF XY: 0.000233 AC XY: 169AN XY: 725604
GnomAD4 genome AF: 0.00151 AC: 230AN: 152258Hom.: 2 Cov.: 32 AF XY: 0.00146 AC XY: 109AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:2
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. -
235-12G>A in intron 3 of LARS2: This variant is not expected to have clinical si gnificance because it has been identified in 0.6% (27/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs75240042). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at