chr2-160280145-A-G

Variant names:

• chr2-160280145-A-G
• rs7572970
• NM_016836.4:c.951+1169T>C

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+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
• Publications: 14 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=-0.9).
• 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 rank	MANE	Protein	UniProt
RBMS1	NM_016836.4	c.951+1169T>C		intron_variant	Intron 10 of 13	ENST00000348849.8	NP_058520.1
RBMS1	NM_002897.5	c.942+1169T>C		intron_variant	Intron 10 of 13		NP_002888.1
RBMS1	XM_047445368.1	c.999+1169T>C		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+1169T>C		intron_variant	Intron 10 of 13	1	NM_016836.4	ENSP00000294904.6

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

African (AFR) AF: 0.623 AC: 25841 AN: 41448

American (AMR) AF: 0.773 AC: 11804 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2011 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4236 AN: 5172

South Asian (SAS) AF: 0.685 AC: 3301 AN: 4816

European-Finnish (FIN) AF: 0.816 AC: 8639 AN: 10584

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.730 AC: 49596 AN: 67982

Other (OTH) AF: 0.693 AC: 1460 AN: 2108

Alfa AF: 0.720 Hom.: 21760

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
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: rs7572970; hg19: chr2-161136656;