NM_001350197.2:c.149+9691A>G

Variant names:

• chr1-92726707-T-C
• rs11578004
• NM_001350197.2:c.149+9691A>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.149+9691A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,118 control chromosomes in the GnomAD database, including 3,538 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 (3538 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.149+9691A>G		intron_variant	Intron 2 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.149+9691A>G		intron_variant	Intron 2 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30359 AN: 152002 Hom.: 3537 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.200 AC: 30372 AN: 152118 Hom.: 3538 Cov.: 32 AF XY: 0.198 AC XY: 14732 AN XY: 74374

African (AFR) AF: 0.106 AC: 4400 AN: 41550

American (AMR) AF: 0.223 AC: 3405 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3468

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5176

South Asian (SAS) AF: 0.126 AC: 609 AN: 4830

European-Finnish (FIN) AF: 0.256 AC: 2708 AN: 10564

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17419 AN: 67944

Other (OTH) AF: 0.229 AC: 484 AN: 2112

Alfa AF: 0.141 Hom.: 324

Bravo AF: 0.192

Asia WGS AF: 0.0910 AC: 320 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.0
DANN	Benign	0.86
PhyloP100		0.54
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: rs11578004; hg19: chr1-93192264;