dbSNP rs2979487: RBPMS:c.66+8952C>G (chr8-30394110-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001008710.3(RBPMS):c.66+8952C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.55 ( 1106 hom., cov: 3)

Consequence

RBPMS
NM_001008710.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364

Publications

1 publications found

Variant links:

Genes affected

RBPMS (HGNC:19097): (RNA binding protein, mRNA processing factor) This gene encodes a member of the RNA recognition motif family of RNA-binding proteins. The RNA recognition motif is between 80-100 amino acids in length and family members contain one to four copies of the motif. The RNA recognition motif consists of two short stretches of conserved sequence, as well as a few highly conserved hydrophobic residues. The encoded protein has a single, putative RNA recognition motif in its N-terminus. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2013]

RBPMS links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001008710.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001008710.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RBPMS	NM_001008710.3	MANE Select	c.66+8952C>G	intron	N/A	NP_001008710.1	Q93062-1
RBPMS	NM_001438067.1		c.66+8952C>G	intron	N/A	NP_001424996.1	B4E3T4
RBPMS	NM_001008712.3		c.66+8952C>G	intron	N/A	NP_001008712.1	Q93062-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RBPMS	ENST00000397323.9	TSL:1 MANE Select	c.66+8952C>G	intron	N/A	ENSP00000380486.4	Q93062-1
RBPMS	ENST00000339877.8	TSL:1	c.66+8952C>G	intron	N/A	ENSP00000340176.4	Q93062-3
RBPMS	ENST00000287771.9	TSL:1	c.66+8952C>G	intron	N/A	ENSP00000287771.5	Q93062-2

Frequencies

GnomAD3 genomes

AF:

0.548

AC:

3497

AN:

6380

Hom.:

1111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.654

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.572

Gnomad EAS

AF:

0.832

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.674

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.575

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.548

AC:

3487

AN:

6366

Hom.:

1106

Cov.:

AF XY:

0.546

AC XY:

1625

AN XY:

2976

show subpopulations

African (AFR)

AF:

0.403

AC:

575

AN:

1428

American (AMR)

AF:

0.584

AC:

425

AN:

728

Ashkenazi Jewish (ASJ)

AF:

0.572

AC:

AN:

152

East Asian (EAS)

AF:

0.833

AC:

360

AN:

432

South Asian (SAS)

AF:

0.419

AC:

177

AN:

422

European-Finnish (FIN)

AF:

0.674

AC:

120

AN:

178

Middle Eastern (MID)

AF:

0.554

AC:

AN:

European-Non Finnish (NFE)

AF:

0.576

AC:

1603

AN:

2782

Other (OTH)

AF:

0.569

AC:

AN:

144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

144

216

288

360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.628

Hom.:

3896

Asia WGS

AF:

0.628

AC:

2183

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.94

(source)

DANN

Benign

0.42

PhyloP100

-0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over