rs1363793

Variant summary

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

The NR_120607.1(LNCBRM):​n.203-229G>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 0.807 in 152,150 control chromosomes in the GnomAD database, including 49,625 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 0.81 ( 49625 hom., cov: 31)

Consequence

LNCBRM
NR_120607.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08
Variant links:
Genes affected
LNCBRM (HGNC:52752): (lncRNA SMARCA2 (BRM) associated)

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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LNCBRMNR_120607.1 linkuse as main transcriptn.203-229G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LNCBRMENST00000664455.1 linkuse as main transcriptn.166-229G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.807
AC:
122661
AN:
152032
Hom.:
49593
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.818
Gnomad AMI
AF:
0.929
Gnomad AMR
AF:
0.785
Gnomad ASJ
AF:
0.799
Gnomad EAS
AF:
0.598
Gnomad SAS
AF:
0.751
Gnomad FIN
AF:
0.810
Gnomad MID
AF:
0.804
Gnomad NFE
AF:
0.823
Gnomad OTH
AF:
0.816
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.807
AC:
122751
AN:
152150
Hom.:
49625
Cov.:
31
AF XY:
0.803
AC XY:
59743
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.818
Gnomad4 AMR
AF:
0.784
Gnomad4 ASJ
AF:
0.799
Gnomad4 EAS
AF:
0.598
Gnomad4 SAS
AF:
0.751
Gnomad4 FIN
AF:
0.810
Gnomad4 NFE
AF:
0.823
Gnomad4 OTH
AF:
0.816
Alfa
AF:
0.811
Hom.:
24072
Bravo
AF:
0.805
Asia WGS
AF:
0.676
AC:
2350
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.019
DANN
Benign
0.55

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: rs1363793; hg19: chr5-56874434; API