rs11953090

Variant names:

• chr5-146257108-T-G
• rs11953090
• NM_018989.2:c.1595-1341T>G

Variant summary

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

The NM_018989.2(RBM27):​c.1595-1341T>G 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 152,214 control chromosomes in the GnomAD database, including 4,258 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 (4258 hom., cov: 32)
• Consequence: RBM27 NM_018989.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM27	NM_018989.2	c.1595-1341T>G		intron_variant	Intron 10 of 20	ENST00000265271.7	NP_061862.1
RBM27-POU4F3	NM_001414499.1	c.1430-1341T>G		intron_variant	Intron 9 of 19		NP_001401428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM27	ENST00000265271.7	c.1595-1341T>G		intron_variant	Intron 10 of 20	1	NM_018989.2	ENSP00000265271.5
ENSG00000275740	ENST00000506502.2	c.1430-1341T>G		intron_variant	Intron 9 of 19	5		ENSP00000475384.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31882 AN: 152096 Hom.: 4244 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.210 AC: 31903 AN: 152214 Hom.: 4258 Cov.: 32 AF XY: 0.211 AC XY: 15683 AN XY: 74404

African (AFR) AF: 0.0508 AC: 2111 AN: 41566

American (AMR) AF: 0.332 AC: 5079 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1159 AN: 5184

South Asian (SAS) AF: 0.163 AC: 784 AN: 4822

European-Finnish (FIN) AF: 0.298 AC: 3146 AN: 10562

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

European-Non Finnish (NFE) AF: 0.267 AC: 18169 AN: 68000

Other (OTH) AF: 0.208 AC: 440 AN: 2116

Alfa AF: 0.249 Hom.: 8574

Bravo AF: 0.210

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.59
PhyloP100		2.1
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: rs11953090; hg19: chr5-145636671;