chr9-106620080-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_104145.1(LINC01505):​n.259+3764G>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 0.151 in 152,194 control chromosomes in the GnomAD database, including 2,448 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 0.15 ( 2448 hom., cov: 33)

Consequence

LINC01505
NR_104145.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.198
Variant links:
Genes affected
LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

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=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC01505NR_104145.1 linkuse as main transcriptn.259+3764G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC01505ENST00000637185.1 linkuse as main transcriptn.760-18079G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.151
AC:
22899
AN:
152076
Hom.:
2439
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.163
Gnomad AMR
AF:
0.0736
Gnomad ASJ
AF:
0.145
Gnomad EAS
AF:
0.0268
Gnomad SAS
AF:
0.333
Gnomad FIN
AF:
0.0575
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.0964
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22941
AN:
152194
Hom.:
2448
Cov.:
33
AF XY:
0.151
AC XY:
11259
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.0734
Gnomad4 ASJ
AF:
0.145
Gnomad4 EAS
AF:
0.0267
Gnomad4 SAS
AF:
0.333
Gnomad4 FIN
AF:
0.0575
Gnomad4 NFE
AF:
0.0964
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.120
Hom.:
826
Bravo
AF:
0.151
Asia WGS
AF:
0.192
AC:
668
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.7
DANN
Benign
0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9942977; hg19: chr9-109382361; API