18-42478917-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_046174.2(LINC00907):n.872+23928T>C 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 0.255 in 152,162 control chromosomes in the GnomAD database, including 6,271 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 0.25 ( 6271 hom., cov: 33)
Consequence
LINC00907
NR_046174.2 intron, non_coding_transcript
NR_046174.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.896
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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC00907 | NR_046174.2 | n.872+23928T>C | intron_variant, non_coding_transcript_variant | ||||
LINC00907 | NR_046454.1 | n.652+23928T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC00907 | ENST00000585627.5 | n.489+23928T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
LINC00907 | ENST00000585639.5 | n.631+23928T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
LINC00907 | ENST00000589068.5 | n.837+23928T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
LINC00907 | ENST00000591381.5 | n.472+23928T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38671AN: 152044Hom.: 6248 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.255 AC: 38743AN: 152162Hom.: 6271 Cov.: 33 AF XY: 0.256 AC XY: 19025AN XY: 74388
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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