11-71969544-C-T

Variant names:

• chr11-71969544-C-T
• rs10501408
• NM_018320.5:c.243+8653C>T

Variant summary

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

The NM_018320.5(RNF121):​c.243+8653C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,198 control chromosomes in the GnomAD database, including 65,308 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 0.92 (65308 hom., cov: 30)
• Consequence: RNF121 NM_018320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 0 publications found

Genes affected

RNF121 (HGNC:21070): (ring finger protein 121) The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Several alternatively spliced transcript variants have been noted for this gene, however, not all are likely to encode viable protein products. [provided by RefSeq, Sep 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF121	NM_018320.5	c.243+8653C>T		intron_variant	Intron 3 of 8	ENST00000361756.8	NP_060790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF121	ENST00000361756.8	c.243+8653C>T		intron_variant	Intron 3 of 8	1	NM_018320.5	ENSP00000354571.3

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140618 AN: 152080 Hom.: 65273 Cov.: 30

Gnomad AFR AF: 0.859

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.925 AC: 140710 AN: 152198 Hom.: 65308 Cov.: 30 AF XY: 0.920 AC XY: 68489 AN XY: 74410

African (AFR) AF: 0.859 AC: 35635 AN: 41484

American (AMR) AF: 0.858 AC: 13106 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3323 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4370 AN: 5174

South Asian (SAS) AF: 0.885 AC: 4270 AN: 4826

European-Finnish (FIN) AF: 0.965 AC: 10242 AN: 10614

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66568 AN: 68026

Other (OTH) AF: 0.945 AC: 1998 AN: 2114

Alfa AF: 0.942 Hom.: 5759

Bravo AF: 0.917

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		0.044
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: rs10501408; hg19: chr11-71680590;