rs1020731

chr2-160287544-G-A

Variant summary

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

The NM_016836.4(RBMS1):c.641-460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,112 control chromosomes in the GnomAD database, including 36,857 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 0.69 (36857 hom., cov: 32)
• Consequence: RBMS1 NM_016836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBMS1	NM_016836.4	c.641-460C>T		intron_variant		ENST00000348849.8
RBMS1	NM_002897.5	c.641-460C>T		intron_variant
RBMS1	XM_047445368.1	c.641-460C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBMS1	ENST00000348849.8	c.641-460C>T		intron_variant		1	NM_016836.4	P1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104966 AN: 151994 Hom.: 36818 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.691 AC: 105055 AN: 152112 Hom.: 36857 Cov.: 32 AF XY: 0.696 AC XY: 51767 AN XY: 74382

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.685

Alfa AF: 0.725 Hom.: 6941

Bravo AF: 0.687

Asia WGS AF: 0.751 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.9
Dann	Benign	0.43

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: rs1020731; hg19: chr2-161144055;