chr1-92662370-A-C

Variant names:

• chr1-92662370-A-C
• rs11800848
• NM_001350197.2:c.1392+349T>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.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
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350197.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	NM_001350197.2	MANE Select	c.1392+349T>G		intron	N/A	NP_001337126.1	A0A804HIC4
	EVI5	NM_001308248.2		c.1377+1050T>G		intron	N/A	NP_001295177.1	O60447-2
	EVI5	NM_001377210.1		c.1368+1050T>G		intron	N/A	NP_001364139.1	A0A9L9PXL1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	ENST00000684568.2	MANE Select	c.1392+349T>G		intron	N/A	ENSP00000506999.1	A0A804HIC4
	EVI5	ENST00000540033.3	TSL:1	c.1377+1050T>G		intron	N/A	ENSP00000440826.2	O60447-2
	EVI5	ENST00000370331.5	TSL:1	c.1344+3569T>G		intron	N/A	ENSP00000359356.1	O60447-1

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

African (AFR) AF: 0.0942 AC: 3912 AN: 41540

American (AMR) AF: 0.224 AC: 3420 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3472

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5184

South Asian (SAS) AF: 0.125 AC: 602 AN: 4832

European-Finnish (FIN) AF: 0.255 AC: 2693 AN: 10556

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17347 AN: 67984

Other (OTH) AF: 0.231 AC: 488 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.63
PhyloP100		1.0
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: rs11800848; hg19: chr1-93127927;