rs4716908

Positions:

• chr7-155768316-T-C
• chr7-155768316-T-G

Variant summary

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

The NM_053043.3(RBM33):​c.3375+1661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,166 control chromosomes in the GnomAD database, including 8,206 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 0.30 (8206 hom., cov: 33)
• Consequence: RBM33 NM_053043.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM33	NM_053043.3	c.3375+1661T>C		intron_variant		ENST00000401878.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM33	ENST00000401878.8	c.3375+1661T>C		intron_variant		5	NM_053043.3	P3
RBM33	ENST00000341148.7	c.183+1661T>C		intron_variant		1		A2
RBM33	ENST00000392755.2	c.100+1661T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44928 AN: 152048 Hom.: 8183 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.296 AC: 45003 AN: 152166 Hom.: 8206 Cov.: 33 AF XY: 0.292 AC XY: 21706 AN XY: 74404

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.285

Alfa AF: 0.194 Hom.: 1647

Bravo AF: 0.312

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.51

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: rs4716908; hg19: chr7-155561010;