rs12743520

Positions:

• chr1-92571555-C-A

Variant summary

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

The NM_001350197.2(EVI5):​c.2071-7818G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,862 control chromosomes in the GnomAD database, including 3,430 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 0.20 (3430 hom., cov: 31)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.2071-7818G>T		intron_variant		ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.2071-7818G>T		intron_variant			NM_001350197.2	ENSP00000506999	P1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29679 AN: 151744 Hom.: 3430 Cov.: 31

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.196 AC: 29692 AN: 151862 Hom.: 3430 Cov.: 31 AF XY: 0.194 AC XY: 14418 AN XY: 74210

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.232

Alfa AF: 0.221 Hom.: 562

Bravo AF: 0.187

Asia WGS AF: 0.0810 AC: 285 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.61
DANN	Benign	0.54

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: rs12743520; hg19: chr1-93037112;