rs1155848

Positions:

• chr13-79314341-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449987.6(RBM26):​c.*629A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 151,758 control chromosomes in the GnomAD database, including 710 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 0.077 (710 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: RBM26 ENST00000449987.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

RBM26 (HGNC:20327): (RNA binding motif protein 26) Enables RNA binding activity. Predicted to be involved in mRNA processing. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM26	XM_005266497.3	c.*629A>G		3_prime_UTR_variant	22/22		XP_005266554.1
RBM26	XM_006719857.3	c.*629A>G		3_prime_UTR_variant	22/22		XP_006719920.1
RBM26	XM_047430510.1	c.*629A>G		3_prime_UTR_variant	22/22		XP_047286466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM26	ENST00000449987.6	c.*629A>G		3_prime_UTR_variant	5/5	3		ENSP00000401474.2

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11617 AN: 151640 Hom.: 705 Cov.: 32

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.0758

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0767 AC: 11634 AN: 151758 Hom.: 710 Cov.: 32 AF XY: 0.0828 AC XY: 6143 AN XY: 74170

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0985

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0991

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.0823

Gnomad4 OTH AF: 0.0793

Alfa AF: 0.0805 Hom.: 604

Bravo AF: 0.0671

Asia WGS AF: 0.163 AC: 564 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.97
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1155848; hg19: chr13-79888476;