rs7225855

chr17-76228324-T-Cchr17-76228324-T-G

Variant summary

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

The NM_052916.3(RNF157):c.88+11829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,896 control chromosomes in the GnomAD database, including 18,525 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 0.49 (18525 hom., cov: 30)
• Consequence: RNF157 NM_052916.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.50

Genes affected

RNF157 (HGNC:29402): (ring finger protein 157) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of signal transduction; positive regulation of dendrite extension; and protein autoubiquitination. Predicted to be located in cell body. Predicted to be active in early endosome; nucleus; and plasma membrane. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF157	NM_052916.3	c.88+11829A>G		intron_variant		ENST00000269391.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF157	ENST00000269391.11	c.88+11829A>G		intron_variant		1	NM_052916.3	P4
RNF157	ENST00000319945.10	c.88+11829A>G		intron_variant		2
RNF157	ENST00000592271.1	c.88+11829A>G		intron_variant		2
RNF157	ENST00000647930.1	c.88+11829A>G		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73637 AN: 151776 Hom.: 18492 Cov.: 30

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.485 AC: 73727 AN: 151896 Hom.: 18525 Cov.: 30 AF XY: 0.484 AC XY: 35936 AN XY: 74220

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.491

Alfa AF: 0.477 Hom.: 3201

Bravo AF: 0.494

Asia WGS AF: 0.399 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.064
Dann	Benign	0.66

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: rs7225855; hg19: chr17-74224405;