12-56535560-C-T

Variant summary

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

The NM_002898.4(RBMS2):​c.66+13471C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 150,878 control chromosomes in the GnomAD database, including 14,764 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 0.42 ( 14764 hom., cov: 29)

Consequence

RBMS2
NM_002898.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0220
Variant links:
Genes affected
RBMS2 (HGNC:9909): (RNA binding motif single stranded interacting protein 2) The protein encoded by this gene is a member of a small family of proteins which bind single stranded DNA/RNA. These proteins are characterized by the presence of two sets of ribonucleoprotein consensus sequence (RNP-CS) that contain conserved motifs, RNP1 and RNP2, originally described in RNA binding proteins, and required for DNA binding. The RBMS proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. This protein was isolated by phenotypic complementation of cdc2 and cdc13 mutants of yeast and is thought to suppress cdc2 and cdc13 mutants through the induction of translation of cdc2. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RBMS2NM_002898.4 linkuse as main transcriptc.66+13471C>T intron_variant ENST00000262031.10 NP_002889.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RBMS2ENST00000262031.10 linkuse as main transcriptc.66+13471C>T intron_variant 1 NM_002898.4 ENSP00000262031 P1

Frequencies

GnomAD3 genomes
AF:
0.416
AC:
62788
AN:
150768
Hom.:
14759
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.191
Gnomad AMI
AF:
0.397
Gnomad AMR
AF:
0.523
Gnomad ASJ
AF:
0.569
Gnomad EAS
AF:
0.598
Gnomad SAS
AF:
0.313
Gnomad FIN
AF:
0.470
Gnomad MID
AF:
0.420
Gnomad NFE
AF:
0.506
Gnomad OTH
AF:
0.474
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.416
AC:
62804
AN:
150878
Hom.:
14764
Cov.:
29
AF XY:
0.413
AC XY:
30384
AN XY:
73540
show subpopulations
Gnomad4 AFR
AF:
0.190
Gnomad4 AMR
AF:
0.523
Gnomad4 ASJ
AF:
0.569
Gnomad4 EAS
AF:
0.599
Gnomad4 SAS
AF:
0.314
Gnomad4 FIN
AF:
0.470
Gnomad4 NFE
AF:
0.506
Gnomad4 OTH
AF:
0.470
Alfa
AF:
0.503
Hom.:
19150
Bravo
AF:
0.422
Asia WGS
AF:
0.402
AC:
1398
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.6
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs7314300; hg19: chr12-56929344; API