chr7-155780782-A-T

Position:

• chr7-155780782-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_053043.3(RBM33):​c.*5741A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 150,692 control chromosomes in the GnomAD database, including 65 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 0.030 (65 hom., cov: 31)
  • Exomes 𝑓: 0.042 (0 hom.)
• Consequence: RBM33 NM_053043.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

Genes affected

RBM33 (HGNC:27223): (RNA binding motif protein 33) Enables RNA binding activity. [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=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0298 (4485/150550) while in subpopulation NFE AF= 0.0407 (2756/67646). AF 95% confidence interval is 0.0395. There are 65 homozygotes in gnomad4. There are 2149 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM33	NM_053043.3	c.*5741A>T		3_prime_UTR_variant	18/18	ENST00000401878.8	NP_444271.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM33	ENST00000401878.8	c.*5741A>T		3_prime_UTR_variant	18/18	5	NM_053043.3	ENSP00000384160	P3
RBM33	ENST00000341148.7	c.*5741A>T		3_prime_UTR_variant	5/5	1		ENSP00000341583	A2

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4481 AN: 150436 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.0563

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.0742

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0320

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0286

GnomAD4 exome AF: 0.0423 AC: 6 AN: 142 Hom.: 0 Cov.: 0 AF XY: 0.0513 AC XY: 4 AN XY: 78

Gnomad4 FIN exome AF: 0.0397

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.0298 AC: 4485 AN: 150550 Hom.: 65 Cov.: 31 AF XY: 0.0292 AC XY: 2149 AN XY: 73584

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.0137

Gnomad4 ASJ AF: 0.0742

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0407

Gnomad4 OTH AF: 0.0288

Alfa AF: 0.0534 Hom.: 22

Bravo AF: 0.0399

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.63
DANN	Benign	0.59

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: rs6962201; hg19: chr7-155573476;