7-92529026-C-G

Position:

• chr7-92529026-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.823

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
RBM48	NM_032120.4	c.111+102C>G		intron_variant		ENST00000265732.10	NP_115496.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM48	ENST00000265732.10	c.111+102C>G		intron_variant		1	NM_032120.4	ENSP00000265732.5
RBM48	ENST00000481551.5	c.111+102C>G		intron_variant		1		ENSP00000419242.1
RBM48	ENST00000496410	c.-221C>G		5_prime_UTR_variant	1/3	3		ENSP00000418333.1

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9167 AN: 152144 Hom.: 596 Cov.: 32

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.: 9 AF XY: 0.0420 AC XY: 15515 AN XY: 369126

Gnomad4 AFR exome AF: 0.0910

Gnomad4 AMR exome AF: 0.145

Gnomad4 ASJ exome AF: 0.0684

Gnomad4 EAS exome AF: 0.299

Gnomad4 SAS exome AF: 0.0345

Gnomad4 FIN exome AF: 0.00467

Gnomad4 NFE exome AF: 0.0193

Gnomad4 OTH exome AF: 0.0506

GnomAD4 genome AF: 0.0603 AC: 9175 AN: 152262 Hom.: 598 Cov.: 32 AF XY: 0.0619 AC XY: 4606 AN XY: 74462

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0743

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.00537

Gnomad4 NFE AF: 0.0195

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.00934 Hom.: 4

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

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -
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	-0.78
CADD	Benign	9.3
DANN	Benign	0.76

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

LitVar

Other links and lift over

dbSNP: rs41278794; hg19: chr7-92158340; COSMIC: COSV50407358; COSMIC: COSV50407358;