rs13188370
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_037889.1(LOC285626):n.746-5395T>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 0.0237 in 152,248 control chromosomes in the GnomAD database, including 64 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 0.024 ( 64 hom., cov: 32)
Consequence
LOC285626
NR_037889.1 intron, non_coding_transcript
NR_037889.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.977
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=-0.81).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (3614/152248) while in subpopulation NFE AF= 0.0351 (2384/68004). AF 95% confidence interval is 0.0339. There are 64 homozygotes in gnomad4. There are 1771 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 64 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC285626 | NR_037889.1 | n.746-5395T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000515337.1 | n.746-5395T>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENST00000641150.1 | n.325-5395T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0238 AC: 3614AN: 152130Hom.: 64 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0237 AC: 3614AN: 152248Hom.: 64 Cov.: 32 AF XY: 0.0238 AC XY: 1771AN XY: 74450
GnomAD4 genome
?
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32
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1771
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74450
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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