4-73998833-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_007058140.1(LOC124900715):n.606G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 555,290 control chromosomes in the GnomAD database, including 206,409 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 0.80 ( 50049 hom., cov: 31)
Exomes 𝑓: 0.88 ( 156360 hom. )
Consequence
LOC124900715
XR_007058140.1 non_coding_transcript_exon
XR_007058140.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.428
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC124900715 | XR_007058140.1 | n.606G>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000287037 | ENST00000669992.1 | n.866+35G>C | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.801 AC: 121717AN: 152020Hom.: 50045 Cov.: 31
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GnomAD4 exome AF: 0.878 AC: 353902AN: 403152Hom.: 156360 AF XY: 0.877 AC XY: 186842AN XY: 213030
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GnomAD4 genome AF: 0.800 AC: 121752AN: 152138Hom.: 50049 Cov.: 31 AF XY: 0.804 AC XY: 59799AN XY: 74382
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at