rs2240327

Variant names:

• chr3-50075601-A-G
• rs2240327
• NM_005777.3:c.3246+271A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-50075601-A-G
• chr3-50075601-A-T

Variant summary

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

The NM_005777.3(RBM6):​c.3246+271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,068 control chromosomes in the GnomAD database, including 20,051 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 0.50 (20051 hom., cov: 31)
• Consequence: RBM6 NM_005777.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 37 publications found

Genes affected

RBM6 (HGNC:9903): (RNA binding motif protein 6) Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM6	NM_005777.3	c.3246+271A>G		intron_variant	Intron 20 of 20	ENST00000266022.9	NP_005768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM6	ENST00000266022.9	c.3246+271A>G		intron_variant	Intron 20 of 20	1	NM_005777.3	ENSP00000266022.4

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75726 AN: 151950 Hom.: 20037 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.498 AC: 75773 AN: 152068 Hom.: 20051 Cov.: 31 AF XY: 0.511 AC XY: 37958 AN XY: 74328

African (AFR) AF: 0.359 AC: 14887 AN: 41488

American (AMR) AF: 0.606 AC: 9240 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4448 AN: 5184

South Asian (SAS) AF: 0.769 AC: 3704 AN: 4818

European-Finnish (FIN) AF: 0.551 AC: 5812 AN: 10554

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33750 AN: 67984

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.502 Hom.: 26282

Bravo AF: 0.489

Asia WGS AF: 0.720 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.1
DANN	Benign	0.80
PhyloP100		-0.10
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: rs2240327; hg19: chr3-50113034;