rs11800848

Positions:

• chr1-92662370-A-C

Variant summary

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

The NM_001350197.2(EVI5):​c.1392+349T>G 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 152,170 control chromosomes in the GnomAD database, including 3,466 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 (3466 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVI5	NM_001350197.2	c.1392+349T>G		intron_variant		ENST00000684568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVI5	ENST00000684568.2	c.1392+349T>G		intron_variant			NM_001350197.2	P1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29792 AN: 152052 Hom.: 3465 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.196 AC: 29808 AN: 152170 Hom.: 3466 Cov.: 32 AF XY: 0.195 AC XY: 14487 AN XY: 74386

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.231

Alfa AF: 0.214 Hom.: 645

Bravo AF: 0.188

Asia WGS AF: 0.0840 AC: 294 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.63

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: rs11800848; hg19: chr1-93127927;