ENST00000449987.6:c.*629A>G

Variant names:

• chr13-79314341-T-C
• rs1155848
• ENST00000449987.6:c.*629A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449987.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM26	ENST00000449987.6	TSL:3	c.*629A>G		3_prime_UTR	Exon 5 of 5	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0141 AC: 584 AN: 41514

American (AMR) AF: 0.0985 AC: 1499 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 167 AN: 3466

East Asian (EAS) AF: 0.187 AC: 966 AN: 5160

South Asian (SAS) AF: 0.0991 AC: 478 AN: 4822

European-Finnish (FIN) AF: 0.199 AC: 2107 AN: 10590

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0823 AC: 5567 AN: 67674

Other (OTH) AF: 0.0793 AC: 167 AN: 2106

Alfa AF: 0.0760 Hom.: 915

Bravo AF: 0.0671

Asia WGS AF: 0.163 AC: 564 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.97
DANN	Benign	0.48
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1155848; hg19: chr13-79888476;