chr4-40489170-G-A

Variant names:

• chr4-40489170-G-A
• rs10517543
• NM_001098634.2:c.-154-22471C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RBM47	NM_001098634.2	c.-154-22471C>T		intron_variant	Intron 2 of 6	ENST00000295971.12	NP_001092104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM47	ENST00000295971.12	c.-154-22471C>T		intron_variant	Intron 2 of 6	5	NM_001098634.2	ENSP00000295971.7

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

African (AFR) AF: 0.0759 AC: 3150 AN: 41482

American (AMR) AF: 0.0692 AC: 1057 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1098 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7291 AN: 67998

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.102 Hom.: 1441

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
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10517543; hg19: chr4-40491187;