rs2308135

chr11-66628514-C-CTAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006328.4(RBM14):c.*1847_*1849dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,738 control chromosomes in the GnomAD database, including 15,854 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (15854 hom., cov: 0)
• Consequence: RBM14 NM_006328.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

RBM14 (HGNC:14219): (RNA binding motif protein 14) This gene encodes a ribonucleoprotein that functions as a general nuclear coactivator, and an RNA splicing modulator. This protein contains two RNA recognition motifs (RRM) at the N-terminus, and multiple hexapeptide repeat domain at the C-terminus that interacts with thyroid hormone receptor-binding protein (TRBP), and is required for transcription activation. Alternatively spliced transcript variants encoding different isoforms (with opposing effects on transcription) have been described for this gene. [provided by RefSeq, Oct 2011]

RBM14-RBM4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM14	NM_006328.4	c.*1847_*1849dup		3_prime_UTR_variant	3/3	ENST00000310137.5
RBM14-RBM4	NM_001198845.2	c.337+11458_337+11460dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM14	ENST00000310137.5	c.*1847_*1849dup		3_prime_UTR_variant	3/3	1	NM_006328.4	P3

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65226 AN: 151620 Hom.: 15847 Cov.: 0

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.430 AC: 65231 AN: 151738 Hom.: 15854 Cov.: 0 AF XY: 0.434 AC XY: 32183 AN XY: 74152

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.466

Alfa AF: 0.454 Hom.: 2015

Bravo AF: 0.429

Asia WGS AF: 0.494 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2308135; hg19: chr11-66395985;