17-59953288-G-A

Variant names:

• chr17-59953288-G-A
• rs180514
• NM_016125.4:c.1174-177C>T

Variant summary

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

The NM_016125.4(RNFT1):​c.1174-177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 150,330 control chromosomes in the GnomAD database, including 1,447 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 0.12 (1447 hom., cov: 31)
• Consequence: RNFT1 NM_016125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

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]

ENSG00000267318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt
RNFT1	NM_016125.4	c.1174-177C>T		intron_variant	Intron 8 of 8	ENST00000305783.13	NP_057209.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNFT1	ENST00000305783.13	c.1174-177C>T		intron_variant	Intron 8 of 8	1	NM_016125.4	ENSP00000304670.8
ENSG00000267318	ENST00000591035.1	c.149+7770G>A		intron_variant	Intron 2 of 3	3		ENSP00000468280.1
RNFT1	ENST00000482446.5	n.*335-177C>T		intron_variant	Intron 7 of 7	1		ENSP00000436144.1
RNFT1	ENST00000466544.5	n.*477-177C>T		intron_variant	Intron 6 of 6	2		ENSP00000436533.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18517 AN: 150218 Hom.: 1448 Cov.: 31

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.123 AC: 18503 AN: 150330 Hom.: 1447 Cov.: 31 AF XY: 0.124 AC XY: 9098 AN XY: 73334

African (AFR) AF: 0.0360 AC: 1469 AN: 40758

American (AMR) AF: 0.157 AC: 2364 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 575 AN: 3450

East Asian (EAS) AF: 0.0540 AC: 275 AN: 5092

South Asian (SAS) AF: 0.106 AC: 505 AN: 4750

European-Finnish (FIN) AF: 0.161 AC: 1648 AN: 10244

Middle Eastern (MID) AF: 0.186 AC: 54 AN: 290

European-Non Finnish (NFE) AF: 0.164 AC: 11084 AN: 67706

Other (OTH) AF: 0.138 AC: 287 AN: 2084

Alfa AF: 0.131 Hom.: 192

Bravo AF: 0.118

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.94
PhyloP100		-1.8
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: rs180514; hg19: chr17-58030649;