3-50055776-G-A

Position:

• chr3-50055776-G-A

Variant summary

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

The NM_005777.3(RBM6):​c.1693+1381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,064 control chromosomes in the GnomAD database, including 32,324 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 0.65 (32324 hom., cov: 32)
• Consequence: RBM6 NM_005777.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM6	NM_005777.3	c.1693+1381G>A		intron_variant		ENST00000266022.9	NP_005768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM6	ENST00000266022.9	c.1693+1381G>A		intron_variant		1	NM_005777.3	ENSP00000266022	P1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98060 AN: 151946 Hom.: 32278 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.646 AC: 98160 AN: 152064 Hom.: 32324 Cov.: 32 AF XY: 0.654 AC XY: 48630 AN XY: 74326

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.629

Alfa AF: 0.586 Hom.: 32896

Bravo AF: 0.648

Asia WGS AF: 0.797 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.89
DANN	Benign	0.50

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: rs6762477; hg19: chr3-50093209;