3-53084723-C-T

Variant summary

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

The XM_006713384.4(RFT1):c.*1126G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,082 control chromosomes in the GnomAD database, including 19,777 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 0.49 (19777 hom., cov: 33)
• Consequence: RFT1 XM_006713384.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

Genes affected

RFT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RFT1	XM_006713384.4	c.*1126G>A		3_prime_UTR_variant	12/12
RFT1	XM_011534214.3	c.1209-6895G>A		intron_variant
RFT1	XM_011534215.4	c.1209-6895G>A		intron_variant
RFT1	XR_007095765.1	n.1244-6895G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73733 AN: 151962 Hom.: 19771 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.485 AC: 73766 AN: 152082 Hom.: 19777 Cov.: 33 AF XY: 0.489 AC XY: 36336 AN XY: 74336

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.520

Alfa AF: 0.553 Hom.: 35450

Bravo AF: 0.480

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.2
Dann	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2336725; hg19: chr3-53118739;