rs2979487

chr8-30394110-C-Gchr8-30394110-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBPMS	NM_001008710.3	c.66+8952C>G		intron_variant		ENST00000397323.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBPMS	ENST00000397323.9	c.66+8952C>G		intron_variant		1	NM_001008710.3	P1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 3497 AN: 6380 Hom.: 1111 Cov.: 3

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.: 3 AF XY: 0.546 AC XY: 1625 AN XY: 2976

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.569

Alfa AF: 0.628 Hom.: 3896

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.94
Dann	Benign	0.42

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

Other links and lift over

dbSNP: rs2979487; hg19: chr8-30251626;