rs11953090

chr5-146257108-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC127814297 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
RBM27	NM_018989.2	c.1595-1341T>G		intron_variant		ENST00000265271.7
LOC127814297	NM_001414499.1	c.1430-1341T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM27	ENST00000265271.7	c.1595-1341T>G		intron_variant		1	NM_018989.2	P1

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

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.208

Alfa AF: 0.252 Hom.: 6921

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

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: rs11953090; hg19: chr5-145636671;