rs17128007
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_038919.1(LOC100128993):n.568+1526G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,210 control chromosomes in the GnomAD database, including 148 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 0.034 ( 148 hom., cov: 32)
Consequence
LOC100128993
NR_038919.1 intron, non_coding_transcript
NR_038919.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.73
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC100128993 | NR_038919.1 | n.568+1526G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000520920.5 | n.474+1526G>A | intron_variant, non_coding_transcript_variant | 4 | ||||||
ENST00000517949.5 | n.535+1526G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000518417.1 | n.278+1526G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0342 AC: 5198AN: 152092Hom.: 148 Cov.: 32
GnomAD3 genomes
?
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5198
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152092
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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: 0.0342 AC: 5201AN: 152210Hom.: 148 Cov.: 32 AF XY: 0.0343 AC XY: 2553AN XY: 74412
GnomAD4 genome
?
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AC:
5201
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152210
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32
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2553
AN XY:
74412
Gnomad4 AFR
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Asia WGS
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58
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at