rs10503868

Variant names:

• chr8-30511921-G-A
• rs10503868
• NM_001008710.3:c.397+7485G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RBPMS	NM_001008710.3	c.397+7485G>A		intron_variant	Intron 5 of 8	ENST00000397323.9	NP_001008710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBPMS	ENST00000397323.9	c.397+7485G>A		intron_variant	Intron 5 of 8	1	NM_001008710.3	ENSP00000380486.4

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

African (AFR) AF: 0.117 AC: 4846 AN: 41486

American (AMR) AF: 0.220 AC: 3349 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3464

East Asian (EAS) AF: 0.258 AC: 1333 AN: 5176

South Asian (SAS) AF: 0.158 AC: 761 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1931 AN: 10544

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17412 AN: 67982

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.248 Hom.: 8245

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
PhyloP100		-0.067
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10503868; hg19: chr8-30369438;