chr2-160368147-C-T

Position:

• chr2-160368147-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.76-756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,972 control chromosomes in the GnomAD database, including 43,091 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 0.75 (43091 hom., cov: 31)
• Consequence: RBMS1 NM_016836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBMS1	NM_016836.4	c.76-756G>A		intron_variant		ENST00000348849.8
RBMS1	NM_002897.5	c.76-756G>A		intron_variant
RBMS1	XM_047445368.1	c.76-756G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBMS1	ENST00000348849.8	c.76-756G>A		intron_variant		1	NM_016836.4	P1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113340 AN: 151854 Hom.: 43064 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.746 AC: 113414 AN: 151972 Hom.: 43091 Cov.: 31 AF XY: 0.751 AC XY: 55804 AN XY: 74292

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.762

Alfa AF: 0.754 Hom.: 5423

Bravo AF: 0.741

Asia WGS AF: 0.830 AC: 2882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.013
DANN	Benign	0.59

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: rs11693602; hg19: chr2-161224658;