7-92529464-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_032120.4(RBM48):​c.112-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,520,912 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

RBM48
NM_032120.4 intron

Scores

2
Splicing: ADA: 0.0007020
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.160
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 7-92529464-C-T is Benign according to our data. Variant chr7-92529464-C-T is described in ClinVar as [Benign]. Clinvar id is 1896032.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RBM48NM_032120.4 linkc.112-12C>T intron_variant ENST00000265732.10 NP_115496.2 Q5RL73-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RBM48ENST00000265732.10 linkc.112-12C>T intron_variant 1 NM_032120.4 ENSP00000265732.5 Q5RL73-1
RBM48ENST00000481551.5 linkc.112-12C>T intron_variant 1 ENSP00000419242.1 Q5RL73-2
RBM48ENST00000496410.1 linkc.-63-12C>T intron_variant 3 ENSP00000418333.1 C9J787

Frequencies

GnomAD3 genomes
AF:
0.00147
AC:
224
AN:
152132
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00505
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.000422
AC:
94
AN:
222930
Hom.:
0
AF XY:
0.000396
AC XY:
48
AN XY:
121226
show subpopulations
Gnomad AFR exome
AF:
0.00548
Gnomad AMR exome
AF:
0.000446
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000143
AC:
196
AN:
1368662
Hom.:
0
Cov.:
21
AF XY:
0.000151
AC XY:
103
AN XY:
682148
show subpopulations
Gnomad4 AFR exome
AF:
0.00459
Gnomad4 AMR exome
AF:
0.000440
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000126
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000670
Gnomad4 OTH exome
AF:
0.000561
GnomAD4 genome
AF:
0.00147
AC:
224
AN:
152250
Hom.:
1
Cov.:
32
AF XY:
0.00138
AC XY:
103
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.00503
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.000128
Hom.:
0
Bravo
AF:
0.00175

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 17, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
CADD
Benign
8.3
DANN
Benign
0.85
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00070
dbscSNV1_RF
Benign
0.32
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.

Other links and lift over

dbSNP: rs146588526; hg19: chr7-92158778; API