chr4-40489170-G-A

Position:

• chr4-40489170-G-A

Variant summary

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

The NM_001098634.2(RBM47):​c.-154-22471C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 152,146 control chromosomes in the GnomAD database, including 712 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 0.088 (712 hom., cov: 32)
• Consequence: RBM47 NM_001098634.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

Genes affected

RBM47 (HGNC:30358): (RNA binding motif protein 47) Enables RNA binding activity. Predicted to act upstream of or within cytidine to uridine editing and hematopoietic progenitor cell differentiation. Predicted to be active in nucleus. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM47	NM_001098634.2	c.-154-22471C>T		intron_variant		ENST00000295971.12	NP_001092104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM47	ENST00000295971.12	c.-154-22471C>T		intron_variant		5	NM_001098634.2	ENSP00000295971	P1

Frequencies

GnomAD3 genomes AF: 0.0885 AC: 13462 AN: 152028 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0903

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0884 AC: 13456 AN: 152146 Hom.: 712 Cov.: 32 AF XY: 0.0857 AC XY: 6377 AN XY: 74396

Gnomad4 AFR AF: 0.0759

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.103 Hom.: 1170

Bravo AF: 0.0883

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.33

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: rs10517543; hg19: chr4-40491187;