rs9302998

Positions:

• chr17-76215788-G-A
• chr17-76215788-G-C

Variant summary

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

The NM_052916.3(RNF157):​c.89-3306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,042 control chromosomes in the GnomAD database, including 23,951 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 0.54 (23951 hom., cov: 32)
• Consequence: RNF157 NM_052916.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF157	NM_052916.3	c.89-3306C>T		intron_variant		ENST00000269391.11	NP_443148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF157	ENST00000269391.11	c.89-3306C>T		intron_variant		1	NM_052916.3	ENSP00000269391.4
RNF157	ENST00000647930.1	c.89-3306C>T		intron_variant				ENSP00000497353.1
RNF157	ENST00000319945.10	c.89-3306C>T		intron_variant		2		ENSP00000321837.4
RNF157	ENST00000592271.1	c.89-3306C>T		intron_variant		2		ENSP00000465543.1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82422 AN: 151922 Hom.: 23904 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.543 AC: 82526 AN: 152042 Hom.: 23951 Cov.: 32 AF XY: 0.541 AC XY: 40193 AN XY: 74330

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.538

Alfa AF: 0.467 Hom.: 28054

Bravo AF: 0.556

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.63

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: rs9302998; hg19: chr17-74211869;