Variant 7-92532521-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_032120.4(RBM48):c.420A>C(p.Ala140Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0222 in 1,612,608 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.017 ( 38 hom., cov: 32)

Exomes 𝑓: 0.023 ( 483 hom. )

Consequence

RBM48
NM_032120.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.204

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 made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 7-92532521-A-C is Benign according to our data. Variant chr7-92532521-A-C is described in ClinVar as [Benign]. Clinvar id is 1598936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.204 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM48	NM_032120.4 linkuse as main transcript	c.420A>C	p.Ala140Ala	synonymous_variant	3/5	ENST00000265732.10	NP_115496.2	Q5RL73-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RBM48	ENST00000265732.10 linkuse as main transcript	c.420A>C	p.Ala140Ala	synonymous_variant	3/5	1	NM_032120.4	ENSP00000265732.5	Q5RL73-1
RBM48	ENST00000481551.5 linkuse as main transcript	c.420A>C	p.Ala140Ala	synonymous_variant	3/4	1		ENSP00000419242.1	Q5RL73-2
RBM48	ENST00000496410.1 linkuse as main transcript	c.246A>C	p.Ala82Ala	synonymous_variant	3/3	3		ENSP00000418333.1	C9J787

Frequencies

GnomAD3 genomes

AF:

0.0172

AC:

2619

AN:

152264

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00487

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0176

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00765

Gnomad FIN

AF:

0.0236

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0256

Gnomad OTH

AF:

0.0191

GnomAD3 exomes

AF:

0.0174

AC:

4335

AN:

248916

Hom.:

AF XY:

0.0177

AC XY:

2392

AN XY:

135084

show subpopulations

Gnomad AFR exome

AF:

0.00311

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.0133

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00764

Gnomad FIN exome

AF:

0.0220

Gnomad NFE exome

AF:

0.0259

Gnomad OTH exome

AF:

0.0210

GnomAD4 exome

AF:

0.0227

AC:

33201

AN:

1460226

Hom.:

483

Cov.:

AF XY:

0.0226

AC XY:

16390

AN XY:

726548

show subpopulations

Gnomad4 AFR exome

AF:

0.00419

Gnomad4 AMR exome

AF:

0.0117

Gnomad4 ASJ exome

AF:

0.0141

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00707

Gnomad4 FIN exome

AF:

0.0212

Gnomad4 NFE exome

AF:

0.0260

Gnomad4 OTH exome

AF:

0.0198

GnomAD4 genome

AF:

0.0172

AC:

2617

AN:

152382

Hom.:

Cov.:

AF XY:

0.0172

AC XY:

1283

AN XY:

74520

show subpopulations

Gnomad4 AFR

AF:

0.00486

Gnomad4 AMR

AF:

0.0175

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00766

Gnomad4 FIN

AF:

0.0236

Gnomad4 NFE

AF:

0.0256

Gnomad4 OTH

AF:

0.0189

Alfa

AF:

0.0168

Hom.:

Bravo

AF:

0.0165

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.0283

EpiControl

AF:

0.0278

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 06, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

3.1

DANN

Benign

0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over