chr4-40507504-T-G

Variant names:

• chr4-40507504-T-G
• rs6848632
• NM_001098634.2:c.-155+36918A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098634.2(RBM47):​c.-155+36918A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,158 control chromosomes in the GnomAD database, including 2,206 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 0.16 (2206 hom., cov: 33)
• Consequence: RBM47 NM_001098634.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM47	NM_001098634.2	c.-155+36918A>C		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.-155+36918A>C		intron_variant	Intron 2 of 6	5	NM_001098634.2	ENSP00000295971.7

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23879 AN: 152040 Hom.: 2199 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.157 AC: 23930 AN: 152158 Hom.: 2206 Cov.: 33 AF XY: 0.160 AC XY: 11882 AN XY: 74398

African (AFR) AF: 0.234 AC: 9721 AN: 41494

American (AMR) AF: 0.183 AC: 2798 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1346 AN: 5174

South Asian (SAS) AF: 0.184 AC: 889 AN: 4822

European-Finnish (FIN) AF: 0.0763 AC: 809 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7479 AN: 67992

Other (OTH) AF: 0.142 AC: 299 AN: 2112

Alfa AF: 0.128 Hom.: 3573

Bravo AF: 0.168

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.20
PhyloP100		-0.25
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: rs6848632; hg19: chr4-40509521;