rs10504930

chr8-93732585-C-T

Variant summary

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

The NM_001377960.1(RBM12B):c.*820G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,920 control chromosomes in the GnomAD database, including 9,286 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 0.34 (9286 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RBM12B NM_001377960.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

Genes affected

RBM12B (HGNC:32310): (RNA binding motif protein 12B) Enables RNA binding activity. Predicted to be involved in regulation of RNA splicing. Predicted to be part of ribonucleoprotein complex. Predicted to be active in nucleoplasm. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM12B	NM_001377960.1	c.*820G>A		3_prime_UTR_variant	4/4	ENST00000520560.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM12B	ENST00000520560.6	c.*820G>A		3_prime_UTR_variant	4/4	2	NM_001377960.1	P1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52305 AN: 151802 Hom.: 9277 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.332

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.345 AC: 52340 AN: 151920 Hom.: 9286 Cov.: 32 AF XY: 0.346 AC XY: 25665 AN XY: 74268

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.330

Alfa AF: 0.307 Hom.: 9824

Bravo AF: 0.355

Asia WGS AF: 0.412 AC: 1429 AN: 3474

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	0.63

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: rs10504930; hg19: chr8-94744813;