2-160280145-A-G

Position:

• chr2-160280145-A-G

Variant summary

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

The NM_016836.4(RBMS1):​c.951+1169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,062 control chromosomes in the GnomAD database, including 38,693 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 0.71 (38693 hom., cov: 31)
• Consequence: RBMS1 NM_016836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBMS1	NM_016836.4	c.951+1169T>C		intron_variant		ENST00000348849.8
RBMS1	NM_002897.5	c.942+1169T>C		intron_variant
RBMS1	XM_047445368.1	c.999+1169T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBMS1	ENST00000348849.8	c.951+1169T>C		intron_variant		1	NM_016836.4	P1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107681 AN: 151944 Hom.: 38647 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.709 AC: 107778 AN: 152062 Hom.: 38693 Cov.: 31 AF XY: 0.714 AC XY: 53103 AN XY: 74340

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.693

Alfa AF: 0.721 Hom.: 19791

Bravo AF: 0.705

Asia WGS AF: 0.773 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.77

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: rs7572970; hg19: chr2-161136656;