11-10529559-T-C

Variant names:

• chr11-10529559-T-C
• rs9300104
• NM_016422.4:c.252+1084A>G

Variant summary

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

The NM_016422.4(RNF141):​c.252+1084A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,022 control chromosomes in the GnomAD database, including 32,165 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 0.65 (32165 hom., cov: 32)
• Consequence: RNF141 NM_016422.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF141	NM_016422.4	c.252+1084A>G		intron_variant	Intron 3 of 5	ENST00000265981.7	NP_057506.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF141	ENST00000265981.7	c.252+1084A>G		intron_variant	Intron 3 of 5	1	NM_016422.4	ENSP00000265981.2
RNF141	ENST00000528665.5	c.252+1084A>G		intron_variant	Intron 3 of 4	2		ENSP00000434320.1
RNF141	ENST00000533412.5	c.252+1084A>G		intron_variant	Intron 3 of 4	5		ENSP00000435086.1
RNF141	ENST00000530156.1	n.*282+1084A>G		intron_variant	Intron 4 of 4	3		ENSP00000437167.1

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98430 AN: 151902 Hom.: 32158 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.648 AC: 98485 AN: 152022 Hom.: 32165 Cov.: 32 AF XY: 0.651 AC XY: 48383 AN XY: 74300

African (AFR) AF: 0.616 AC: 25530 AN: 41444

American (AMR) AF: 0.714 AC: 10915 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2244 AN: 3468

East Asian (EAS) AF: 0.845 AC: 4379 AN: 5180

South Asian (SAS) AF: 0.739 AC: 3563 AN: 4822

European-Finnish (FIN) AF: 0.622 AC: 6557 AN: 10546

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43312 AN: 67964

Other (OTH) AF: 0.611 AC: 1290 AN: 2110

Alfa AF: 0.649 Hom.: 11072

Bravo AF: 0.656

Asia WGS AF: 0.753 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.58
PhyloP100		-0.85
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: rs9300104; hg19: chr11-10551106;