rs13155119

Variant names:

• chr5-146262444-T-C
• rs13155119
• NM_018989.2:c.2190+638T>C

Variant summary

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

The NM_018989.2(RBM27):​c.2190+638T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,164 control chromosomes in the GnomAD database, including 4,248 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 0.21 (4248 hom., cov: 32)
• Consequence: RBM27 NM_018989.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 9 publications found

Genes affected

RBM27 (HGNC:29243): (RNA binding motif protein 27) Enables RNA binding activity. Predicted to be involved in mRNA processing. Predicted to be located in cytoplasm and nuclear speck. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000275740 (HGNC:58349):

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 (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018989.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM27	NM_018989.2	MANE Select	c.2190+638T>C		intron	N/A	NP_061862.1
	RBM27-POU4F3	NM_001414499.1		c.2025+638T>C		intron	N/A	NP_001401428.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM27	ENST00000265271.7	TSL:1 MANE Select	c.2190+638T>C		intron	N/A	ENSP00000265271.5
	ENSG00000275740	ENST00000506502.2	TSL:5	c.2025+638T>C		intron	N/A	ENSP00000475384.1
	RBM27	ENST00000508019.1	TSL:3	n.424+638T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31870 AN: 152046 Hom.: 4234 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31891 AN: 152164 Hom.: 4248 Cov.: 32 AF XY: 0.211 AC XY: 15662 AN XY: 74366

African (AFR) AF: 0.0509 AC: 2114 AN: 41536

American (AMR) AF: 0.332 AC: 5081 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5166

South Asian (SAS) AF: 0.163 AC: 787 AN: 4828

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18163 AN: 68006

Other (OTH) AF: 0.209 AC: 442 AN: 2114

Alfa AF: 0.249 Hom.: 8561

Bravo AF: 0.210

Asia WGS AF: 0.188 AC: 656 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.097
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: rs13155119; hg19: chr5-145642007; COSMIC: COSV54592365;