rs1616547

Variant names:

• chr13-79411901-A-C
• rs1616547
• ENST00000606049.1:n.131-781A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-79411901-A-C
• chr13-79411901-A-T

Variant summary

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

The ENST00000606049.1(RBM26-AS1):​n.131-781A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,054 control chromosomes in the GnomAD database, including 16,229 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 0.46 (16229 hom., cov: 32)
• Consequence: RBM26-AS1 ENST00000606049.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 3 publications found

Genes affected

RBM26-AS1 (HGNC:39805): (RBM26 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606049.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM26-AS1	NR_038991.1		n.170-781A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM26-AS1	ENST00000606049.1	TSL:1	n.131-781A>C		intron	N/A
	RBM26-AS1	ENST00000456602.5	TSL:2	n.170-781A>C		intron	N/A
	RBM26-AS1	ENST00000607864.1	TSL:3	n.732+4806A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69234 AN: 151936 Hom.: 16224 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.455 AC: 69254 AN: 152054 Hom.: 16229 Cov.: 32 AF XY: 0.451 AC XY: 33533 AN XY: 74340

African (AFR) AF: 0.390 AC: 16181 AN: 41454

American (AMR) AF: 0.390 AC: 5952 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2068 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1572 AN: 5154

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4380 AN: 10588

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35023 AN: 67974

Other (OTH) AF: 0.462 AC: 974 AN: 2108

Alfa AF: 0.344 Hom.: 934

Bravo AF: 0.447

Asia WGS AF: 0.407 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1616547; hg19: chr13-79986036;