rs1481847

Variant summary

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

The NR_033652.1(MSC-AS1):​n.776+24838G>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 0.557 in 151,942 control chromosomes in the GnomAD database, including 23,681 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 0.56 ( 23681 hom., cov: 32)

Consequence

MSC-AS1
NR_033652.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.584
Variant links:
Genes affected
MSC-AS1 (HGNC:48724): (MSC antisense RNA 1)

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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MSC-AS1NR_033652.1 linkuse as main transcriptn.776+24838G>A intron_variant, non_coding_transcript_variant
MSC-AS1NR_033651.1 linkuse as main transcriptn.307+24838G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MSC-AS1ENST00000518916.5 linkuse as main transcriptn.265+24838G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.557
AC:
84620
AN:
151824
Hom.:
23654
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.554
Gnomad AMI
AF:
0.410
Gnomad AMR
AF:
0.516
Gnomad ASJ
AF:
0.623
Gnomad EAS
AF:
0.589
Gnomad SAS
AF:
0.508
Gnomad FIN
AF:
0.583
Gnomad MID
AF:
0.675
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.552
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.557
AC:
84689
AN:
151942
Hom.:
23681
Cov.:
32
AF XY:
0.555
AC XY:
41221
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.554
Gnomad4 AMR
AF:
0.516
Gnomad4 ASJ
AF:
0.623
Gnomad4 EAS
AF:
0.589
Gnomad4 SAS
AF:
0.507
Gnomad4 FIN
AF:
0.583
Gnomad4 NFE
AF:
0.564
Gnomad4 OTH
AF:
0.556
Alfa
AF:
0.541
Hom.:
9167
Bravo
AF:
0.555
Asia WGS
AF:
0.613
AC:
2134
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.24
DANN
Benign
0.49

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: rs1481847; hg19: chr8-72781495; API