12-15322057-T-TCA
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The XR_007063224.1(LOC105369673):n.332+15319_332+15320insTG 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 0.00758 in 152,206 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0076 ( 9 hom., cov: 32)
Consequence
LOC105369673
XR_007063224.1 intron, non_coding_transcript
XR_007063224.1 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.152
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-15322057-T-TCA is Benign according to our data. Variant chr12-15322057-T-TCA is described in ClinVar as [Likely_benign]. Clinvar id is 1707139.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00758 (1153/152206) while in subpopulation AFR AF= 0.0255 (1060/41512). AF 95% confidence interval is 0.0243. There are 9 homozygotes in gnomad4. There are 558 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105369673 | XR_007063224.1 | n.332+15319_332+15320insTG | intron_variant, non_coding_transcript_variant | |||||
LOC105369673 | XR_007063225.1 | n.2298_2299insTG | non_coding_transcript_exon_variant | 3/3 | ||||
LOC105369673 | XR_007063226.1 | n.2327_2328insTG | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RERG | ENST00000393736.3 | c.-115+15319_-115+15320insTG | intron_variant | 3 | ENSP00000440887 |
Frequencies
GnomAD3 genomes AF: 0.00755 AC: 1149AN: 152088Hom.: 9 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00758 AC: 1153AN: 152206Hom.: 9 Cov.: 32 AF XY: 0.00750 AC XY: 558AN XY: 74426
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 26, 2020 | See Variant Classification Assertion Criteria. - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at