dbSNP rs1060586: RBM18:c.*484C>T (chr9-122241400-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_033117.4(RBM18):c.*484C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,570 control chromosomes in the GnomAD database, including 17,902 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 0.47 ( 17828 hom., cov: 33)

Exomes 𝑓: 0.53 ( 74 hom. )

Consequence

RBM18
NM_033117.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.637

Publications

14 publications found

Variant links:

Genes affected

RBM18 (HGNC:28413): (RNA binding motif protein 18) Predicted to enable RNA binding activity. Located in cytosol; intercellular bridge; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

RBM18 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
RBM18	NM_033117.4 link	c.*484C>T	3_prime_UTR_variant	Exon 6 of 6	ENST00000417201.4	NP_149108.1
RBM18	NR_027125.2 link	n.1324C>T	non_coding_transcript_exon_variant	Exon 7 of 7
RBM18	NR_027126.2 link	n.1293C>T	non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM18	ENST00000417201.4 link	c.*484C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_033117.4	ENSP00000409315.2

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71798

AN:

151894

Hom.:

17833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.543

Gnomad EAS

AF:

0.831

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.502

GnomAD4 exome

AF:

0.534

AC:

298

AN:

558

Hom.:

Cov.:

AF XY:

0.529

AC XY:

180

AN XY:

340

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.700

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.560

AC:

223

AN:

398

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.445

AC:

AN:

128

Other (OTH)

AF:

0.375

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.472

AC:

71815

AN:

152012

Hom.:

17828

Cov.:

AF XY:

0.476

AC XY:

35345

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.324

AC:

13428

AN:

41464

American (AMR)

AF:

0.540

AC:

8248

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.543

AC:

1881

AN:

3462

East Asian (EAS)

AF:

0.831

AC:

4313

AN:

5188

South Asian (SAS)

AF:

0.508

AC:

2449

AN:

4822

European-Finnish (FIN)

AF:

0.510

AC:

5378

AN:

10540

Middle Eastern (MID)

AF:

0.449

AC:

131

AN:

292

European-Non Finnish (NFE)

AF:

0.509

AC:

34583

AN:

67952

Other (OTH)

AF:

0.500

AC:

1054

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1904

3807

5711

7614

9518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

654

1308

1962

2616

3270

<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:

0.504

Hom.:

35439

Bravo

AF:

0.469

Asia WGS

AF:

0.634

AC:

2206

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.9

(source)

DANN

Benign

0.58

PhyloP100

0.64

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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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