rs17657688

chr3-49995795-T-C

Variant summary

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

The NM_005777.3(RBM6):c.1484-3645T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,994 control chromosomes in the GnomAD database, including 12,044 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 0.39 (12044 hom., cov: 31)
• Consequence: RBM6 NM_005777.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM6	NM_005777.3	c.1484-3645T>C		intron_variant		ENST00000266022.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM6	ENST00000266022.9	c.1484-3645T>C		intron_variant		1	NM_005777.3	P1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59214 AN: 151876 Hom.: 12035 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.390 AC: 59243 AN: 151994 Hom.: 12044 Cov.: 31 AF XY: 0.380 AC XY: 28238 AN XY: 74278

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.391

Alfa AF: 0.407 Hom.: 2649

Bravo AF: 0.393

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.7
Dann	Benign	0.73

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: rs17657688; hg19: chr3-50033228;