rs10503868

Positions:

• chr8-30511921-G-A

Variant summary

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

The NM_001008710.3(RBPMS):​c.397+7485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,044 control chromosomes in the GnomAD database, including 3,553 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 0.21 (3553 hom., cov: 31)
• Consequence: RBPMS NM_001008710.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBPMS	NM_001008710.3	c.397+7485G>A		intron_variant		ENST00000397323.9	NP_001008710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBPMS	ENST00000397323.9	c.397+7485G>A		intron_variant		1	NM_001008710.3	ENSP00000380486	P1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31439 AN: 151926 Hom.: 3547 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.207 AC: 31453 AN: 152044 Hom.: 3553 Cov.: 31 AF XY: 0.203 AC XY: 15097 AN XY: 74340

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.240

Alfa AF: 0.254 Hom.: 6735

Bravo AF: 0.208

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.44

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: rs10503868; hg19: chr8-30369438;