rs4669638
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NR_110575.1(LINC01954):n.178+3161T>A 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 0.00105 in 152,240 control chromosomes in the GnomAD database, including 3 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 0.0011 ( 3 hom., cov: 33)
Consequence
LINC01954
NR_110575.1 intron, non_coding_transcript
NR_110575.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.939
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS2
?
High Homozygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01954 | NR_110575.1 | n.178+3161T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01954 | ENST00000607419.1 | n.176+3161T>A | intron_variant, non_coding_transcript_variant | 1 | |||||
LINC01954 | ENST00000691398.1 | n.283-3229T>A | intron_variant, non_coding_transcript_variant | ||||||
LINC01954 | ENST00000652896.1 | n.470-3229T>A | intron_variant, non_coding_transcript_variant | ||||||
LINC01954 | ENST00000670239.2 | n.446+3161T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00105 AC: 159AN: 152122Hom.: 3 Cov.: 33
GnomAD3 genomes
?
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159
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152122
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00105 AC: 160AN: 152240Hom.: 3 Cov.: 33 AF XY: 0.00120 AC XY: 89AN XY: 74450
GnomAD4 genome
?
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AC:
160
AN:
152240
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33
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89
AN XY:
74450
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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