rs10929981

chr2-160377284-C-T

Variant summary

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

The NM_016836.4(RBMS1):c.76-9893G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,116 control chromosomes in the GnomAD database, including 45,156 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 0.76 (45156 hom., cov: 33)
• Consequence: RBMS1 NM_016836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594

Genes affected

RBMS1 (HGNC:9907): (RNA binding motif single stranded interacting protein 1) This gene encodes 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. These proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. Several transcript variants, resulting from alternative splicing and encoding different isoforms, have been described. A pseudogene for this locus is found on chromosome 12. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBMS1	NM_016836.4	c.76-9893G>A		intron_variant		ENST00000348849.8
RBMS1	NM_002897.5	c.76-9893G>A		intron_variant
RBMS1	XM_047445368.1	c.76-9893G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBMS1	ENST00000348849.8	c.76-9893G>A		intron_variant		1	NM_016836.4	P1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116176 AN: 151998 Hom.: 45119 Cov.: 33

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.764 AC: 116265 AN: 152116 Hom.: 45156 Cov.: 33 AF XY: 0.769 AC XY: 57205 AN XY: 74364

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.768

Alfa AF: 0.801 Hom.: 22293

Bravo AF: 0.758

Asia WGS AF: 0.852 AC: 2955 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.3
Dann	Benign	0.62

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: rs10929981; hg19: chr2-161233795;