chr2-160280479-T-C

Variant names:

• chr2-160280479-T-C
• rs716615
• NM_016836.4:c.951+835A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016836.4(RBMS1):​c.951+835A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,108 control chromosomes in the GnomAD database, including 8,175 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 0.32 (8175 hom., cov: 32)
• Consequence: RBMS1 NM_016836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBMS1	NM_016836.4	c.951+835A>G		intron_variant	Intron 10 of 13	ENST00000348849.8	NP_058520.1
RBMS1	NM_002897.5	c.942+835A>G		intron_variant	Intron 10 of 13		NP_002888.1
RBMS1	XM_047445368.1	c.999+835A>G		intron_variant	Intron 11 of 13		XP_047301324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBMS1	ENST00000348849.8	c.951+835A>G		intron_variant	Intron 10 of 13	1	NM_016836.4	ENSP00000294904.6

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49032 AN: 151990 Hom.: 8168 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.323 AC: 49066 AN: 152108 Hom.: 8175 Cov.: 32 AF XY: 0.327 AC XY: 24302 AN XY: 74356

African (AFR) AF: 0.305 AC: 12651 AN: 41508

American (AMR) AF: 0.278 AC: 4233 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2751 AN: 5186

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4824

European-Finnish (FIN) AF: 0.410 AC: 4336 AN: 10566

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22254 AN: 67984

Other (OTH) AF: 0.313 AC: 662 AN: 2116

Alfa AF: 0.319 Hom.: 2409

Bravo AF: 0.319

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.50
PhyloP100		0.17
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: rs716615; hg19: chr2-161136990;