rs3768331

chr1-228094994-C-T

Variant summary

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

The NM_001658.4(ARF1):c.-37-2084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,938 control chromosomes in the GnomAD database, including 8,711 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 0.33 (8711 hom., cov: 31)
• Consequence: ARF1 NM_001658.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

ARF1 (HGNC:652): (ADP ribosylation factor 1) ADP-ribosylation factor 1 (ARF1) is a member of the human ARF gene family. The family members encode small guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin and play a role in vesicular trafficking as activators of phospholipase D. The gene products, including 6 ARF proteins and 11 ARF-like proteins, constitute a family of the RAS superfamily. The ARF proteins are categorized as class I (ARF1, ARF2 and ARF3), class II (ARF4 and ARF5) and class III (ARF6), and members of each class share a common gene organization. The ARF1 protein is localized to the Golgi apparatus and has a central role in intra-Golgi transport. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARF1	NM_001658.4	c.-37-2084C>T		intron_variant		ENST00000272102.10
ARF1	NM_001024226.2	c.-37-2084C>T		intron_variant
ARF1	NM_001024227.1	c.-37-2084C>T		intron_variant
ARF1	NM_001024228.2	c.-37-2084C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARF1	ENST00000272102.10	c.-37-2084C>T		intron_variant		1	NM_001658.4	P1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49584 AN: 151818 Hom.: 8702 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.326 AC: 49606 AN: 151938 Hom.: 8711 Cov.: 31 AF XY: 0.329 AC XY: 24397 AN XY: 74236

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.356

Alfa AF: 0.383 Hom.: 15140

Bravo AF: 0.323

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.46

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: rs3768331; hg19: chr1-228282695;