NM_016422.4:c.-47-2847G>C

Variant names:

• chr11-10537052-C-G
• rs2054392
• NM_016422.4:c.-47-2847G>C

Variant summary

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

The NM_016422.4(RNF141):​c.-47-2847G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,124 control chromosomes in the GnomAD database, including 10,476 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 0.35 (10476 hom., cov: 33)
• Consequence: RNF141 NM_016422.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 5 publications found

Genes affected

RNF141 (HGNC:21159): (ring finger protein 141) The protein encoded by this gene contains a RING finger, a motif known to be involved in protein-DNA and protein-protein interactions. Abundant expression of this gene was found in the testicular tissue of fertile men, but was not detected in azoospermic patients. Studies of the mouse counterpart suggest that this gene may function as a testis specific transcription factor during spermatogenesis. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF141	NM_016422.4	c.-47-2847G>C		intron_variant	Intron 1 of 5	ENST00000265981.7	NP_057506.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF141	ENST00000265981.7	c.-47-2847G>C		intron_variant	Intron 1 of 5	1	NM_016422.4	ENSP00000265981.2
RNF141	ENST00000528665.5	c.-47-2847G>C		intron_variant	Intron 1 of 4	2		ENSP00000434320.1
RNF141	ENST00000533412.5	c.-47-2847G>C		intron_variant	Intron 1 of 4	5		ENSP00000435086.1
RNF141	ENST00000530156.1	n.-47-2847G>C		intron_variant	Intron 1 of 4	3		ENSP00000437167.1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53235 AN: 152004 Hom.: 10475 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.350 AC: 53248 AN: 152124 Hom.: 10476 Cov.: 33 AF XY: 0.353 AC XY: 26230 AN XY: 74366

African (AFR) AF: 0.181 AC: 7504 AN: 41512

American (AMR) AF: 0.421 AC: 6448 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3468

East Asian (EAS) AF: 0.658 AC: 3410 AN: 5182

South Asian (SAS) AF: 0.347 AC: 1676 AN: 4824

European-Finnish (FIN) AF: 0.394 AC: 4156 AN: 10556

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27555 AN: 67966

Other (OTH) AF: 0.331 AC: 699 AN: 2114

Alfa AF: 0.219 Hom.: 531

Bravo AF: 0.354

Asia WGS AF: 0.453 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.20
DANN	Benign	0.84
PhyloP100		-0.95
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: rs2054392; hg19: chr11-10558599;