rs1415296

Variant names:

• chr1-92624919-G-C
• rs1415296
• NM_001350197.2:c.1669-585C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350197.2(EVI5):​c.1669-585C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,130 control chromosomes in the GnomAD database, including 3,525 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 (3525 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.1669-585C>G		intron_variant	Intron 15 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.1669-585C>G		intron_variant	Intron 15 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29993 AN: 152012 Hom.: 3525 Cov.: 32

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0240

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.197 AC: 30003 AN: 152130 Hom.: 3525 Cov.: 32 AF XY: 0.196 AC XY: 14559 AN XY: 74354

African (AFR) AF: 0.0944 AC: 3924 AN: 41550

American (AMR) AF: 0.225 AC: 3434 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3466

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5190

South Asian (SAS) AF: 0.126 AC: 607 AN: 4828

European-Finnish (FIN) AF: 0.256 AC: 2694 AN: 10522

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17507 AN: 67984

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.221 Hom.: 513

Bravo AF: 0.189

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.1
DANN	Benign	0.83
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1415296; hg19: chr1-93090476;