rs438259
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000642760.1(HULC):n.1054-16317G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,040 control chromosomes in the GnomAD database, including 5,820 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 0.27 ( 5820 hom., cov: 32)
Consequence
HULC
ENST00000642760.1 intron
ENST00000642760.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.15
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105374914 | XR_001743951.1 | n.585-16317G>A | intron_variant | |||||
LOC105374914 | XR_001743952.1 | n.279-16317G>A | intron_variant | |||||
LOC105374914 | XR_001743953.1 | n.279-16317G>A | intron_variant | |||||
LOC105374914 | XR_926450.3 | n.401-16317G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HULC | ENST00000642760.1 | n.1054-16317G>A | intron_variant | |||||||
HULC | ENST00000642798.1 | n.821-16317G>A | intron_variant | |||||||
HULC | ENST00000642877.1 | n.112-16317G>A | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.274 AC: 41663AN: 151922Hom.: 5812 Cov.: 32
GnomAD3 genomes
AF:
AC:
41663
AN:
151922
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.274 AC: 41696AN: 152040Hom.: 5820 Cov.: 32 AF XY: 0.273 AC XY: 20282AN XY: 74286
GnomAD4 genome
AF:
AC:
41696
AN:
152040
Hom.:
Cov.:
32
AF XY:
AC XY:
20282
AN XY:
74286
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
915
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at