rs7225855

Variant names:

• chr17-76228324-T-C
• rs7225855
• NM_052916.3:c.88+11829A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-76228324-T-C
• chr17-76228324-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RNF157	NM_052916.3	c.88+11829A>G		intron_variant	Intron 1 of 18	ENST00000269391.11	NP_443148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF157	ENST00000269391.11	c.88+11829A>G		intron_variant	Intron 1 of 18	1	NM_052916.3	ENSP00000269391.4
RNF157	ENST00000647930.1	c.88+11829A>G		intron_variant	Intron 1 of 18			ENSP00000497353.1
RNF157	ENST00000319945.10	c.88+11829A>G		intron_variant	Intron 1 of 17	2		ENSP00000321837.4
RNF157	ENST00000592271.1	c.88+11829A>G		intron_variant	Intron 1 of 1	2		ENSP00000465543.1

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

African (AFR) AF: 0.610 AC: 25274 AN: 41438

American (AMR) AF: 0.474 AC: 7234 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2369 AN: 5142

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4818

European-Finnish (FIN) AF: 0.426 AC: 4493 AN: 10540

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29567 AN: 67912

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.481 Hom.: 3349

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
PhyloP100		-5.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs7225855; hg19: chr17-74224405;