rs77878271
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The ENST00000524085.2(ENSG00000253859):n.299-14617A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.0191 in 474,530 control chromosomes in the GnomAD database, including 133 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 0.016 ( 35 hom., cov: 32)
Exomes 𝑓: 0.020 ( 98 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.39
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0163 (2488/152258) while in subpopulation NFE AF= 0.0224 (1523/68004). AF 95% confidence interval is 0.0215. There are 35 homozygotes in gnomad4. There are 1291 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 35 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101927118 | XR_001745980.2 | n.517+21326A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000524085.2 | n.299-14617A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0163 AC: 2485AN: 152140Hom.: 35 Cov.: 32
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GnomAD4 exome AF: 0.0204 AC: 6582AN: 322272Hom.: 98 Cov.: 5 AF XY: 0.0200 AC XY: 3331AN XY: 166470
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GnomAD4 genome ? AF: 0.0163 AC: 2488AN: 152258Hom.: 35 Cov.: 32 AF XY: 0.0173 AC XY: 1291AN XY: 74438
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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