dbSNP rs2308135: RBM14:c.*1847_*1849dupTAA (chr11-66628514-C-CTAA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006328.4(RBM14):c.*1847_*1849dupTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 15854 hom., cov: 0)

Consequence

RBM14
NM_006328.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.257

Publications

5 publications found

Variant links:

Genes affected

RBM14 (HGNC:14219): (RNA binding motif protein 14) This gene encodes a ribonucleoprotein that functions as a general nuclear coactivator, and an RNA splicing modulator. This protein contains two RNA recognition motifs (RRM) at the N-terminus, and multiple hexapeptide repeat domain at the C-terminus that interacts with thyroid hormone receptor-binding protein (TRBP), and is required for transcription activation. Alternatively spliced transcript variants encoding different isoforms (with opposing effects on transcription) have been described for this gene. [provided by RefSeq, Oct 2011]

RBM14 links:

RBM14-RBM4 (HGNC:38840): (RBM14-RBM4 readthrough) This locus represents naturally occurring read-through transcription between the neighboring RBM14 (RNA binding motif protein 14) and RBM4 (RNA binding motif protein 4) genes. Alternative splicing results in multiple transcript variants, one of which encodes a fusion protein that shares sequence identity with each individual gene product. This fusion protein contains RRM and zinc finger domains, and it functions to stimulate transcription in a hormone and receptor-dependent manner. [provided by RefSeq, Nov 2010]

RBM14-RBM4 links:

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new If you want to explore the variant's impact on the transcript NM_006328.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006328.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RBM14	NM_006328.4	MANE Select	c.1847_1849dupTAA	3_prime_UTR	Exon 3 of 3	NP_006319.1	A0A0S2Z4Z0
RBM14	NM_001198836.2		c.2032_2034dupTAA	3_prime_UTR	Exon 3 of 3	NP_001185765.1	A0A0S2Z567
RBM14	NM_001198837.2		c.2032_2034dupTAA	3_prime_UTR	Exon 2 of 2	NP_001185766.1	Q96PK6-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RBM14	ENST00000310137.5	TSL:1 MANE Select	c.1847_1849dupTAA	3_prime_UTR	Exon 3 of 3	ENSP00000311747.5	Q96PK6-1
RBM14-RBM4	ENST00000412278.2	TSL:2	c.337+11458_337+11460dupTAA	intron	N/A	ENSP00000388552.2
RBM14-RBM4	ENST00000500635.2	TSL:2	c.337+11458_337+11460dupTAA	intron	N/A	ENSP00000421279.1

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65226

AN:

151620

Hom.:

15847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.627

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.442

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.462

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

GnomAD4 genome

AF:

0.430

AC:

65231

AN:

151738

Hom.:

15854

Cov.:

AF XY:

0.434

AC XY:

32183

AN XY:

74152

show subpopulations

African (AFR)

AF:

0.181

AC:

7513

AN:

41406

American (AMR)

AF:

0.594

AC:

9038

AN:

15216

Ashkenazi Jewish (ASJ)

AF:

0.497

AC:

1723

AN:

3466

East Asian (EAS)

AF:

0.456

AC:

2353

AN:

5164

South Asian (SAS)

AF:

0.600

AC:

2887

AN:

4814

European-Finnish (FIN)

AF:

0.442

AC:

4649

AN:

10516

Middle Eastern (MID)

AF:

0.497

AC:

146

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35370

AN:

67846

Other (OTH)

AF:

0.466

AC:

981

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1711

3422

5133

6844

8555

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<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:

0.454

Hom.:

2015

Bravo

AF:

0.429

Asia WGS

AF:

0.494

AC:

1716

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over