9-122241400-G-A

Position:

• chr9-122241400-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033117.4(RBM18):​c.*484C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,570 control chromosomes in the GnomAD database, including 17,902 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 0.47 (17828 hom., cov: 33)
  • Exomes 𝑓: 0.53 (74 hom.)
• Consequence: RBM18 NM_033117.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

Genes affected

RBM18 (HGNC:28413): (RNA binding motif protein 18) Predicted to enable RNA binding activity. Located in cytosol; intercellular bridge; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM18	NM_033117.4	c.*484C>T		3_prime_UTR_variant	6/6	ENST00000417201.4
RBM18	NR_027125.2	n.1324C>T		non_coding_transcript_exon_variant	7/7
RBM18	NR_027126.2	n.1293C>T		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM18	ENST00000417201.4	c.*484C>T		3_prime_UTR_variant	6/6	1	NM_033117.4	P1

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71798 AN: 151894 Hom.: 17833 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.534 AC: 298 AN: 558 Hom.: 74 Cov.: 0 AF XY: 0.529 AC XY: 180 AN XY: 340

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.700

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.560

Gnomad4 NFE exome AF: 0.445

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.472 AC: 71815 AN: 152012 Hom.: 17828 Cov.: 33 AF XY: 0.476 AC XY: 35345 AN XY: 74310

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.500

Alfa AF: 0.509 Hom.: 26187

Bravo AF: 0.469

Asia WGS AF: 0.634 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs1060586; hg19: chr9-125003679; COSMIC: COSV69874092; COSMIC: COSV69874092;