rs180511

chr17-59955087-G-A

Variant summary

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

The NM_016125.4(RNFT1):c.1072-941C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,124 control chromosomes in the GnomAD database, including 1,693 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 0.14 (1693 hom., cov: 32)
• Consequence: RNFT1 NM_016125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

RNFT1 (HGNC:30206): (ring finger protein, transmembrane 1) Enables ubiquitin binding activity and ubiquitin protein ligase activity. Involved in positive regulation of ERAD pathway and protein autoubiquitination. Located in endoplasmic reticulum. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNFT1	NM_016125.4	c.1072-941C>T		intron_variant		ENST00000305783.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNFT1	ENST00000305783.13	c.1072-941C>T		intron_variant		1	NM_016125.4	P1
RNFT1	ENST00000482446.5	c.*233-941C>T		intron_variant, NMD_transcript_variant		1
RNFT1	ENST00000466544.5	c.*375-941C>T		intron_variant, NMD_transcript_variant		2
RNFT1	ENST00000486103.6	n.573-941C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21617 AN: 152006 Hom.: 1694 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.142 AC: 21608 AN: 152124 Hom.: 1693 Cov.: 32 AF XY: 0.142 AC XY: 10573 AN XY: 74362

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0536

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.152

Alfa AF: 0.151 Hom.: 209

Bravo AF: 0.141

Asia WGS AF: 0.0770 AC: 269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.0
Dann	Benign	0.72

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: rs180511; hg19: chr17-58032448;