rs2242071
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NR_038437.1(LOC100507443):n.98-7083C>T 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 0.72 in 780,104 control chromosomes in the GnomAD database, including 204,984 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.72 ( 39520 hom., cov: 32)
Exomes 𝑓: 0.72 ( 165464 hom. )
Consequence
LOC100507443
NR_038437.1 intron, non_coding_transcript
NR_038437.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.628
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=-0.28).
BP6
?
Variant 2-208129973-C-T is Benign according to our data. Variant chr2-208129973-C-T is described in ClinVar as [Benign]. Clinvar id is 1291617.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC100507443 | NR_038437.1 | n.98-7083C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.718 AC: 109099AN: 151982Hom.: 39478 Cov.: 32
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GnomAD4 exome AF: 0.721 AC: 452796AN: 628004Hom.: 165464 AF XY: 0.723 AC XY: 243845AN XY: 337154
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GnomAD4 genome ? AF: 0.718 AC: 109198AN: 152100Hom.: 39520 Cov.: 32 AF XY: 0.715 AC XY: 53176AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at