rs13132688
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000500358.6(ENSG00000246090):n.428+736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00479 in 152,228 control chromosomes in the GnomAD database, including 1 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 0.0048 ( 1 hom., cov: 32)
Consequence
ENSG00000246090
ENST00000500358.6 intron
ENST00000500358.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.107
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC100507053 | NR_037884.1 | n.428+736G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000246090 | ENST00000500358.6 | n.428+736G>A | intron_variant | 1 | ||||||
ENSG00000246090 | ENST00000499178.2 | n.334+736G>A | intron_variant | 3 | ||||||
ENSG00000246090 | ENST00000661393.1 | n.425+736G>A | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00479 AC: 729AN: 152110Hom.: 1 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: 0.00479 AC: 729AN: 152228Hom.: 1 Cov.: 32 AF XY: 0.00484 AC XY: 360AN XY: 74432
GnomAD4 genome
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729
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32
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360
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74432
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at