rs9302997

Variant names:

• chr17-76215763-T-A
• rs9302997
• NM_052916.3:c.89-3281A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-76215763-T-A
• chr17-76215763-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052916.3(RNF157):​c.89-3281A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,050 control chromosomes in the GnomAD database, including 7,538 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 (7538 hom., cov: 32)
• Consequence: RNF157 NM_052916.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052916.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF157	NM_052916.3	MANE Select	c.89-3281A>T		intron	N/A	NP_443148.1
	RNF157	NM_001438721.1		c.89-3281A>T		intron	N/A	NP_001425650.1
	RNF157	NM_001330501.2		c.89-3281A>T		intron	N/A	NP_001317430.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF157	ENST00000269391.11	TSL:1 MANE Select	c.89-3281A>T		intron	N/A	ENSP00000269391.4
	RNF157	ENST00000647930.1		c.89-3281A>T		intron	N/A	ENSP00000497353.1
	RNF157	ENST00000319945.10	TSL:2	c.89-3281A>T		intron	N/A	ENSP00000321837.4

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45739 AN: 151932 Hom.: 7537 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.301 AC: 45761 AN: 152050 Hom.: 7538 Cov.: 32 AF XY: 0.303 AC XY: 22481 AN XY: 74314

African (AFR) AF: 0.179 AC: 7422 AN: 41500

American (AMR) AF: 0.273 AC: 4166 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2380 AN: 5168

South Asian (SAS) AF: 0.275 AC: 1326 AN: 4824

European-Finnish (FIN) AF: 0.375 AC: 3957 AN: 10552

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24330 AN: 67944

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.328 Hom.: 1125

Bravo AF: 0.290

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.062
DANN	Benign	0.62
PhyloP100		-3.0
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: rs9302997; hg19: chr17-74211844;