Genetic Variant RBM17:c.931-206T>C (chr10-6113843-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 NM_032905.5(RBM17):c.931-206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 586,974 control chromosomes in the GnomAD database, including 23,412 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 0.22 ( 4735 hom., cov: 33)

Exomes 𝑓: 0.28 ( 18677 hom. )

Consequence

RBM17
NM_032905.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.834

Publications

7 publications found

Variant links:

Genes affected

RBM17 (HGNC:16944): (RNA binding motif protein 17) This gene encodes an RNA binding protein. The encoded protein is part of the spliceosome complex and functions in the second catalytic step of mRNA splicing. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 9 and 15. [provided by RefSeq, Mar 2009]

RBM17 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM17	NM_032905.5 link	c.931-206T>C		intron_variant	Intron 9 of 11	ENST00000379888.9	NP_116294.1	Q96I25Q5W009
RBM17	NM_001145547.2 link	c.931-206T>C		intron_variant	Intron 9 of 11		NP_001139019.1	Q96I25Q5W009

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM17	ENST00000379888.9 link	c.931-206T>C		intron_variant	Intron 9 of 11	1	NM_032905.5	ENSP00000369218.4		Q96I25

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33851

AN:

152156

Hom.:

4734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0598

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.275

GnomAD4 exome

AF:

0.284

AC:

123325

AN:

434700

Hom.:

18677

AF XY:

0.287

AC XY:

65755

AN XY:

229048

show subpopulations

African (AFR)

AF:

0.0625

AC:

764

AN:

12218

American (AMR)

AF:

0.285

AC:

4490

AN:

15766

Ashkenazi Jewish (ASJ)

AF:

0.448

AC:

6003

AN:

13398

East Asian (EAS)

AF:

0.159

AC:

4828

AN:

30440

South Asian (SAS)

AF:

0.302

AC:

12569

AN:

41624

European-Finnish (FIN)

AF:

0.239

AC:

7493

AN:

31352

Middle Eastern (MID)

AF:

0.355

AC:

681

AN:

1920

European-Non Finnish (NFE)

AF:

0.302

AC:

79395

AN:

262784

Other (OTH)

AF:

0.282

AC:

7102

AN:

25198

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

4146

8292

12438

16584

20730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.222

AC:

33850

AN:

152274

Hom.:

4735

Cov.:

AF XY:

0.220

AC XY:

16414

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0597

AC:

2481

AN:

41578

American (AMR)

AF:

0.250

AC:

3831

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

1523

AN:

3470

East Asian (EAS)

AF:

0.176

AC:

915

AN:

5186

South Asian (SAS)

AF:

0.294

AC:

1417

AN:

4824

European-Finnish (FIN)

AF:

0.225

AC:

2387

AN:

10596

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.300

AC:

20417

AN:

68004

Other (OTH)

AF:

0.275

AC:

582

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1308

2616

3924

5232

6540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.264

Hom.:

2149

Bravo

AF:

0.217

Asia WGS

AF:

0.231

AC:

805

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.1

(source)

DANN

Benign

0.49

PhyloP100

-0.83

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