Genetic Variant RBM11:n.1064T>C (chr21-14227444-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000468643.5(RBM11):n.1064T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 858,740 control chromosomes in the GnomAD database, including 76,533 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 0.43 ( 13838 hom., cov: 32)

Exomes 𝑓: 0.42 ( 62695 hom. )

Consequence

RBM11
ENST00000468643.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.825

Publications

8 publications found

Variant links:

Genes affected

RBM11 (HGNC:9897): (RNA binding motif protein 11) Enables poly(U) RNA binding activity and protein homodimerization activity. Acts upstream of or within cellular response to oxidative stress and regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

RBM11 links:

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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=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM11	NM_144770.5 link	c.*151T>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000400577.4	NP_658983.3	P57052-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
RBM11	ENST00000468643.5 link	n.1064T>C	non_coding_transcript_exon_variant	Exon 5 of 5	1
RBM11	ENST00000495055.1 link	n.868T>C	non_coding_transcript_exon_variant	Exon 4 of 4	1
RBM11	ENST00000400577.4 link	c.*151T>C	3_prime_UTR_variant	Exon 5 of 5	1	NM_144770.5	ENSP00000383421.3	P57052-1
RBM11	ENST00000475864.1 link	n.*60T>C	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64577

AN:

151858

Hom.:

13829

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.460

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.401

Gnomad MID

AF:

0.474

Gnomad NFE

AF:

0.413

Gnomad OTH

AF:

0.427

GnomAD4 exome

AF:

0.422

AC:

298005

AN:

706764

Hom.:

62695

Cov.:

AF XY:

0.424

AC XY:

150391

AN XY:

354400

show subpopulations

African (AFR)

AF:

0.432

AC:

7258

AN:

16790

American (AMR)

AF:

0.426

AC:

5874

AN:

13800

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

6504

AN:

14780

East Asian (EAS)

AF:

0.510

AC:

15597

AN:

30582

South Asian (SAS)

AF:

0.498

AC:

19424

AN:

39022

European-Finnish (FIN)

AF:

0.403

AC:

11944

AN:

29634

Middle Eastern (MID)

AF:

0.437

AC:

1097

AN:

2512

European-Non Finnish (NFE)

AF:

0.410

AC:

215698

AN:

525514

Other (OTH)

AF:

0.428

AC:

14609

AN:

34130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

8381

16762

25142

33523

41904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.425

AC:

64620

AN:

151976

Hom.:

13838

Cov.:

AF XY:

0.425

AC XY:

31567

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.433

AC:

17956

AN:

41460

American (AMR)

AF:

0.424

AC:

6471

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.460

AC:

1596

AN:

3466

East Asian (EAS)

AF:

0.518

AC:

2676

AN:

5168

South Asian (SAS)

AF:

0.485

AC:

2343

AN:

4826

European-Finnish (FIN)

AF:

0.401

AC:

4237

AN:

10558

Middle Eastern (MID)

AF:

0.476

AC:

138

AN:

290

European-Non Finnish (NFE)

AF:

0.413

AC:

28056

AN:

67944

Other (OTH)

AF:

0.424

AC:

891

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1933

3866

5799

7732

9665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.419

Hom.:

11721

Bravo

AF:

0.428

Asia WGS

AF:

0.484

AC:

1680

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

0.82

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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21-14227444-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over