rs10784460

Variant summary

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

The NR_120431.1(MSRB3-AS1):​n.550-2670C>T 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 0.368 in 152,006 control chromosomes in the GnomAD database, including 11,002 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 0.37 ( 11002 hom., cov: 32)

Consequence

MSRB3-AS1
NR_120431.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.56
Variant links:
Genes affected
MSRB3-AS1 (HGNC:53386): (MSRB3 antisense RNA 1)
MSRB3 (HGNC:27375): (methionine sulfoxide reductase B3) The protein encoded by this gene catalyzes the reduction of methionine sulfoxide to methionine. This enzyme acts as a monomer and requires zinc as a cofactor. Several transcript variants encoding two different isoforms have been found for this gene. One of the isoforms localizes to mitochondria while the other localizes to endoplasmic reticula. [provided by RefSeq, Jul 2010]

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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MSRB3-AS1NR_120431.1 linkuse as main transcriptn.550-2670C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MSRB3-AS1ENST00000537250.5 linkuse as main transcriptn.376-2670C>T intron_variant, non_coding_transcript_variant 3
MSRB3ENST00000446731.2 linkuse as main transcriptc.265+15979G>A intron_variant 3 ENSP00000404903
MSRB3ENST00000541189.5 linkuse as main transcriptc.436+15979G>A intron_variant 3 ENSP00000440722
MSRB3ENST00000647481.1 linkuse as main transcriptc.195+15979G>A intron_variant ENSP00000496162

Frequencies

GnomAD3 genomes
AF:
0.368
AC:
55919
AN:
151890
Hom.:
10997
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.233
Gnomad AMI
AF:
0.450
Gnomad AMR
AF:
0.290
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.449
Gnomad SAS
AF:
0.341
Gnomad FIN
AF:
0.386
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.453
Gnomad OTH
AF:
0.392
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.368
AC:
55936
AN:
152006
Hom.:
11002
Cov.:
32
AF XY:
0.367
AC XY:
27243
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.233
Gnomad4 AMR
AF:
0.290
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.449
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.386
Gnomad4 NFE
AF:
0.453
Gnomad4 OTH
AF:
0.392
Alfa
AF:
0.291
Hom.:
1005
Bravo
AF:
0.356
Asia WGS
AF:
0.357
AC:
1239
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.062
DANN
Benign
0.74

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: rs10784460; hg19: chr12-65863584; API