rs16894959
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_017754.4(BLTP3A):āc.1735T>Cā(p.Leu579=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,613,712 control chromosomes in the GnomAD database, including 17,853 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.17 ( 2597 hom., cov: 32)
Exomes š: 0.14 ( 15256 hom. )
Consequence
BLTP3A
NM_017754.4 synonymous
NM_017754.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.431
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
?
Synonymous conserved (PhyloP=-0.431 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLTP3A | NM_017754.4 | c.1735T>C | p.Leu579= | synonymous_variant | 13/21 | ENST00000192788.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLTP3A | ENST00000192788.6 | c.1735T>C | p.Leu579= | synonymous_variant | 13/21 | 1 | NM_017754.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.174 AC: 26422AN: 151990Hom.: 2593 Cov.: 32
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GnomAD3 exomes AF: 0.131 AC: 32626AN: 249234Hom.: 2642 AF XY: 0.129 AC XY: 17437AN XY: 135222
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GnomAD4 exome AF: 0.138 AC: 202302AN: 1461604Hom.: 15256 Cov.: 33 AF XY: 0.137 AC XY: 99503AN XY: 727082
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GnomAD4 genome ? AF: 0.174 AC: 26440AN: 152108Hom.: 2597 Cov.: 32 AF XY: 0.175 AC XY: 12990AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at