7-155780782-A-T

Variant names:

• chr7-155780782-A-T
• rs6962201
• NM_053043.3:c.*5741A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

RBM33 (HGNC:27223): (RNA binding motif protein 33) Enables RNA binding activity. [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=-0.83).
• 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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053043.3. 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
	RBM33	NM_053043.3	MANE Select	c.*5741A>T		3_prime_UTR	Exon 18 of 18	NP_444271.2	Q96EV2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM33	ENST00000401878.8	TSL:5 MANE Select	c.*5741A>T		3_prime_UTR	Exon 18 of 18	ENSP00000384160.3	Q96EV2-1
	RBM33	ENST00000341148.7	TSL:1	c.*5741A>T		3_prime_UTR	Exon 5 of 5	ENSP00000341583.3	A0A0C4DFS3

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

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) AF: 0.0397 AC: 5 AN: 126

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10

Other (OTH) AF: 0.167 AC: 1 AN: 6

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

African (AFR) AF: 0.0159 AC: 645 AN: 40620

American (AMR) AF: 0.0137 AC: 208 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0742 AC: 256 AN: 3448

East Asian (EAS) AF: 0.0156 AC: 79 AN: 5052

South Asian (SAS) AF: 0.0322 AC: 154 AN: 4776

European-Finnish (FIN) AF: 0.0251 AC: 265 AN: 10546

Middle Eastern (MID) AF: 0.0379 AC: 11 AN: 290

European-Non Finnish (NFE) AF: 0.0407 AC: 2756 AN: 67646

Other (OTH) AF: 0.0288 AC: 60 AN: 2082

Alfa AF: 0.0534 Hom.: 22

Bravo AF: 0.0399

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.63
DANN	Benign	0.59
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism

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: rs6962201; hg19: chr7-155573476;