Genetic Variant RBM26-AS1:n.131-781A>C (chr13-79411901-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180

Publications

3 publications found

Variant links:

Genes affected

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

RBM26-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM26-AS1	NR_038991.1 link	n.170-781A>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
RBM26-AS1	ENST00000606049.1 link	n.131-781A>C	intron_variant	Intron 1 of 6	1
RBM26-AS1	ENST00000456602.5 link	n.170-781A>C	intron_variant	Intron 1 of 5	2
RBM26-AS1	ENST00000607864.1 link	n.732+4806A>C	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.456

AC:

69234

AN:

151936

Hom.:

16224

Cov.:

show subpopulations

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.:

AF XY:

0.451

AC XY:

33533

AN XY:

74340

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1913

3825

5738

7650

9563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

0.18

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over