rs6841061
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_002959837.1(LOC105377588):n.890C>T 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 0.608 in 518,070 control chromosomes in the GnomAD database, including 97,392 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 0.63 ( 30631 hom., cov: 33)
Exomes 𝑓: 0.60 ( 66761 hom. )
Consequence
LOC105377588
XR_002959837.1 non_coding_transcript_exon
XR_002959837.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.423
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105377588 | XR_002959837.1 | n.890C>T | non_coding_transcript_exon_variant | 2/3 | |||
LINC02436 | NR_174108.1 | n.404-7395G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02436 | ENST00000509017.6 | n.1499+6316G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.630 AC: 95744AN: 152012Hom.: 30601 Cov.: 33
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GnomAD3 exomes AF: 0.589 AC: 134859AN: 228804Hom.: 40869 AF XY: 0.593 AC XY: 75011AN XY: 126436
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GnomAD4 exome AF: 0.598 AC: 218973AN: 365940Hom.: 66761 Cov.: 0 AF XY: 0.599 AC XY: 125683AN XY: 209812
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GnomAD4 genome ? AF: 0.630 AC: 95822AN: 152130Hom.: 30631 Cov.: 33 AF XY: 0.623 AC XY: 46319AN XY: 74358
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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