rs3900
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NR_045128.1(TXLNGY):n.125+889G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.43 ( 0 hom., 14199 hem., cov: 0)
Failed GnomAD Quality Control
Consequence
TXLNGY
NR_045128.1 intron, non_coding_transcript
NR_045128.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.86
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXLNGY | NR_045128.1 | n.125+889G>C | intron_variant, non_coding_transcript_variant | ||||
TXLNGY | NR_045129.1 | n.125+889G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXLNGY | ENST00000445715.6 | n.101+889G>C | intron_variant, non_coding_transcript_variant | ||||||
TXLNGY | ENST00000700762.1 | n.195+801G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.431 AC: 14145AN: 32811Hom.: 0 Cov.: 0 AF XY: 0.431 AC XY: 14145AN XY: 32811
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.432 AC: 14199AN: 32874Hom.: 0 Cov.: 0 AF XY: 0.432 AC XY: 14199AN XY: 32874
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?
Data not reliable, filtered out with message: InbreedingCoeff
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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