rs7134216
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015054.2(BLTP3B):c.44+16621G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,020 control chromosomes in the GnomAD database, including 8,241 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: 𝑓 0.28 ( 8241 hom., cov: 32)
Consequence
BLTP3B
NM_015054.2 intron
NM_015054.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.05
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLTP3B | NM_015054.2 | c.44+16621G>A | intron_variant | ENST00000279907.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLTP3B | ENST00000279907.12 | c.44+16621G>A | intron_variant | 1 | NM_015054.2 | P1 | |||
BLTP3B | ENST00000356828.7 | c.44+16621G>A | intron_variant | 1 | |||||
BLTP3B | ENST00000547428.1 | c.*52+2609G>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.275 AC: 41765AN: 151902Hom.: 8208 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.275 AC: 41854AN: 152020Hom.: 8241 Cov.: 32 AF XY: 0.267 AC XY: 19863AN XY: 74320
GnomAD4 genome
?
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152020
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32
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19863
AN XY:
74320
Gnomad4 AFR
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Asia WGS
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625
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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