rs4847267

chr1-92689790-C-T

Variant summary

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

The NM_001350197.2(EVI5):c.1097+4012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,064 control chromosomes in the GnomAD database, including 29,380 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 0.61 (29380 hom., cov: 33)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

EVI5 (HGNC:3501): (ecotropic viral integration site 5) Enables GTPase activator activity and small GTPase binding activity. Involved in positive regulation of GTPase activity and retrograde transport, endosome to Golgi. Located in cytosol. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVI5	NM_001350197.2	c.1097+4012G>A		intron_variant		ENST00000684568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVI5	ENST00000684568.2	c.1097+4012G>A		intron_variant			NM_001350197.2	P1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93134 AN: 151946 Hom.: 29376 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.613 AC: 93177 AN: 152064 Hom.: 29380 Cov.: 33 AF XY: 0.617 AC XY: 45891 AN XY: 74336

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.588

Alfa AF: 0.631 Hom.: 4661

Bravo AF: 0.609

Asia WGS AF: 0.797 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.9
Dann	Benign	0.40

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: rs4847267; hg19: chr1-93155347;