chr5-146233607-GCCAGGTCCAGGCCCAGGCCCGGGC-G

Position:

• chr5-146233607-GCCAGGTCCAGGCCCAGGCCCGGGC-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6 BS2

The NM_018989.2(RBM27):​c.1044_1067delCCCAGGCCCGGGCCCAGGTCCAGG​(p.Pro349_Gly356del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00174 in 1,607,722 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0018 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0017 (5 hom.)
• Consequence: RBM27 NM_018989.2 disruptive_inframe_deletion
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 6.47

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:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP6: Variant 5-146233607-GCCAGGTCCAGGCCCAGGCCCGGGC-G is Benign according to our data. Variant chr5-146233607-GCCAGGTCCAGGCCCAGGCCCGGGC-G is described in ClinVar as [Likely_benign]. Clinvar id is 3050808.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 264 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM27	NM_018989.2	c.1044_1067delCCCAGGCCCGGGCCCAGGTCCAGG	p.Pro349_Gly356del	disruptive_inframe_deletion	7/21	ENST00000265271.7	NP_061862.1
LOC127814297	NM_001414499.1	c.1044_1067delCCCAGGCCCGGGCCCAGGTCCAGG	p.Pro349_Gly356del	disruptive_inframe_deletion	7/20		NP_001401428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM27	ENST00000265271.7	c.1044_1067delCCCAGGCCCGGGCCCAGGTCCAGG	p.Pro349_Gly356del	disruptive_inframe_deletion	7/21	1	NM_018989.2	ENSP00000265271.5
ENSG00000275740	ENST00000506502.2	c.1044_1067delCCCAGGCCCGGGCCCAGGTCCAGG	p.Pro349_Gly356del	disruptive_inframe_deletion	7/20	5		ENSP00000475384.1

Frequencies

GnomAD3 genomes AF: 0.00176 AC: 264 AN: 150236 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00210

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000994

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00139

Gnomad SAS AF: 0.00234

Gnomad FIN AF: 0.000487

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00191

Gnomad OTH AF: 0.00391

GnomAD3 exomes AF: 0.00181 AC: 449 AN: 248020 Hom.: 1 AF XY: 0.00184 AC XY: 248 AN XY: 134856

Gnomad AFR exome AF: 0.00195

Gnomad AMR exome AF: 0.00196

Gnomad ASJ exome AF: 0.000300

Gnomad EAS exome AF: 0.00185

Gnomad SAS exome AF: 0.00177

Gnomad FIN exome AF: 0.000325

Gnomad NFE exome AF: 0.00210

Gnomad OTH exome AF: 0.00299

GnomAD4 exome AF: 0.00174 AC: 2536 AN: 1457364 Hom.: 5 AF XY: 0.00176 AC XY: 1279 AN XY: 725188

Gnomad4 AFR exome AF: 0.00210

Gnomad4 AMR exome AF: 0.00191

Gnomad4 ASJ exome AF: 0.000422

Gnomad4 EAS exome AF: 0.00172

Gnomad4 SAS exome AF: 0.00190

Gnomad4 FIN exome AF: 0.000412

Gnomad4 NFE exome AF: 0.00179

Gnomad4 OTH exome AF: 0.00191

GnomAD4 genome AF: 0.00176 AC: 264 AN: 150358 Hom.: 0 Cov.: 31 AF XY: 0.00162 AC XY: 119 AN XY: 73370

Gnomad4 AFR AF: 0.00210

Gnomad4 AMR AF: 0.000992

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00139

Gnomad4 SAS AF: 0.00234

Gnomad4 FIN AF: 0.000487

Gnomad4 NFE AF: 0.00191

Gnomad4 OTH AF: 0.00387

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

RBM27-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 01, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-145613170;