rs4770336
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_138043.1(LINC00621):n.652+9590G>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 0.517 in 151,816 control chromosomes in the GnomAD database, including 23,123 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 0.52 ( 23123 hom., cov: 32)
Consequence
LINC00621
NR_138043.1 intron, non_coding_transcript
NR_138043.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.117
Genes affected
LINC00621 (HGNC:44227): (long intergenic non-protein coding RNA 621)
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC00621 | NR_138043.1 | n.652+9590G>A | intron_variant, non_coding_transcript_variant | ||||
LOC105370109 | XR_001749785.2 | n.262+2566C>T | intron_variant, non_coding_transcript_variant | ||||
LOC105370109 | XR_941738.1 | n.300+2566C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC00621 | ENST00000668623.1 | n.58+9590G>A | intron_variant, non_coding_transcript_variant | ||||||
ENST00000686188.1 | n.286+2566C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.518 AC: 78531AN: 151698Hom.: 23132 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
78531
AN:
151698
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: 0.517 AC: 78520AN: 151816Hom.: 23123 Cov.: 32 AF XY: 0.520 AC XY: 38611AN XY: 74192
GnomAD4 genome
?
AF:
AC:
78520
AN:
151816
Hom.:
Cov.:
32
AF XY:
AC XY:
38611
AN XY:
74192
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:
1930
AN:
3474
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