rs10504930

Variant names:

• chr8-93732585-C-T
• rs10504930
• NM_001377960.1:c.*820G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

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 = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377960.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM12B	NM_001377960.1	MANE Select	c.*820G>A		3_prime_UTR	Exon 4 of 4	NP_001364889.1	Q8IXT5
	RBM12B	NM_001377961.1		c.*820G>A		3_prime_UTR	Exon 5 of 5	NP_001364890.1	Q8IXT5
	RBM12B	NM_001377962.1		c.*820G>A		3_prime_UTR	Exon 3 of 3	NP_001364891.1	Q8IXT5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM12B	ENST00000520560.6	TSL:2 MANE Select	c.*820G>A		3_prime_UTR	Exon 4 of 4	ENSP00000429807.2	Q8IXT5
	RBM12B	ENST00000517700.6	TSL:1	c.*820G>A		3_prime_UTR	Exon 3 of 3	ENSP00000427729.2	Q8IXT5
	RBM12B	ENST00000399300.7	TSL:2	c.*820G>A		3_prime_UTR	Exon 3 of 3	ENSP00000382239.2	Q8IXT5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.393 AC: 16288 AN: 41412

American (AMR) AF: 0.410 AC: 6266 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3466

East Asian (EAS) AF: 0.501 AC: 2588 AN: 5170

South Asian (SAS) AF: 0.282 AC: 1358 AN: 4822

European-Finnish (FIN) AF: 0.316 AC: 3323 AN: 10528

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20244 AN: 67948

Other (OTH) AF: 0.330 AC: 694 AN: 2102

Alfa AF: 0.313 Hom.: 13783

Bravo AF: 0.355

Asia WGS AF: 0.412 AC: 1429 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.97
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: rs10504930; hg19: chr8-94744813;