Genetic Variant RBM48:c.111+102C>G (chr7-92529026-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032120.4(RBM48):c.111+102C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 852,214 control chromosomes in the GnomAD database, including 2,797 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 598 hom., cov: 32)

Exomes 𝑓: 0.043 ( 2199 hom. )

Consequence

RBM48
NM_032120.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.823

Publications

3 publications found

Variant links:

Genes affected

RBM48 (HGNC:21785): (RNA binding motif protein 48) Predicted to enable RNA binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

RBM48 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 7-92529026-C-G is Benign according to our data. Variant chr7-92529026-C-G is described in ClinVar as [Benign]. Clinvar id is 1229078.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM48	NM_032120.4 link	c.111+102C>G		intron_variant	Intron 1 of 4	ENST00000265732.10	NP_115496.2	Q5RL73-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
RBM48	ENST00000265732.10 link	c.111+102C>G	intron_variant	Intron 1 of 4	1	NM_032120.4	ENSP00000265732.5	Q5RL73-1
RBM48	ENST00000481551.5 link	c.111+102C>G	intron_variant	Intron 1 of 3	1		ENSP00000419242.1	Q5RL73-2
RBM48	ENST00000496410.1 link	c.-221C>G	5_prime_UTR_variant	Exon 1 of 3	3		ENSP00000418333.1	C9J787

Frequencies

GnomAD3 genomes

AF:

0.0603

AC:

9167

AN:

152144

Hom.:

596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0942

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0743

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.0398

Gnomad FIN

AF:

0.00537

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0195

Gnomad OTH

AF:

0.0598

GnomAD4 exome

AF:

0.0435

AC:

30431

AN:

699952

Hom.:

2199

Cov.:

AF XY:

0.0420

AC XY:

15515

AN XY:

369126

show subpopulations

African (AFR)

AF:

0.0910

AC:

1624

AN:

17848

American (AMR)

AF:

0.145

AC:

4670

AN:

32182

Ashkenazi Jewish (ASJ)

AF:

0.0684

AC:

1407

AN:

20582

East Asian (EAS)

AF:

0.299

AC:

9699

AN:

32392

South Asian (SAS)

AF:

0.0345

AC:

2232

AN:

64670

European-Finnish (FIN)

AF:

0.00467

AC:

226

AN:

48424

Middle Eastern (MID)

AF:

0.0474

AC:

204

AN:

4300

European-Non Finnish (NFE)

AF:

0.0193

AC:

8594

AN:

444506

Other (OTH)

AF:

0.0506

AC:

1775

AN:

35048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1330

2660

3989

5319

6649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0603

AC:

9175

AN:

152262

Hom.:

598

Cov.:

AF XY:

0.0619

AC XY:

4606

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.0941

AC:

3910

AN:

41538

American (AMR)

AF:

0.109

AC:

1667

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0743

AC:

258

AN:

3472

East Asian (EAS)

AF:

0.303

AC:

1566

AN:

5168

South Asian (SAS)

AF:

0.0396

AC:

191

AN:

4824

European-Finnish (FIN)

AF:

0.00537

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0195

AC:

1324

AN:

68024

Other (OTH)

AF:

0.0596

AC:

126

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

403

806

1210

1613

2016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00934

Hom.:

Bravo

AF:

0.0721

Asia WGS

AF:

0.154

AC:

535

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

May 16, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.3

(source)

DANN

Benign

0.76

PhyloP100

0.82

PromoterAI

-0.062

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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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7-92529026-C-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over