chr1-92568466-G-T

Variant names:

• chr1-92568466-G-T
• rs1556562
• NM_001350197.2:c.2071-4729C>A

Variant summary

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

The NM_001350197.2(EVI5):​c.2071-4729C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,100 control chromosomes in the GnomAD database, including 55,545 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 0.85 (55545 hom., cov: 30)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 13 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	NM_001350197.2	MANE Select	c.2071-4729C>A		intron	N/A	NP_001337126.1
	EVI5	NM_001308248.2		c.2056-4729C>A		intron	N/A	NP_001295177.1
	EVI5	NM_001377210.1		c.2047-4729C>A		intron	N/A	NP_001364139.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVI5	ENST00000684568.2	MANE Select	c.2071-4729C>A		intron	N/A	ENSP00000506999.1
	EVI5	ENST00000540033.3	TSL:1	c.2056-4729C>A		intron	N/A	ENSP00000440826.2
	EVI5	ENST00000370331.5	TSL:1	c.2023-4729C>A		intron	N/A	ENSP00000359356.1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129427 AN: 151984 Hom.: 55488 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.852 AC: 129545 AN: 152100 Hom.: 55545 Cov.: 30 AF XY: 0.854 AC XY: 63487 AN XY: 74338

African (AFR) AF: 0.927 AC: 38496 AN: 41510

American (AMR) AF: 0.869 AC: 13273 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3077 AN: 3468

East Asian (EAS) AF: 0.968 AC: 5023 AN: 5188

South Asian (SAS) AF: 0.952 AC: 4586 AN: 4818

European-Finnish (FIN) AF: 0.766 AC: 8071 AN: 10538

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54253 AN: 67982

Other (OTH) AF: 0.838 AC: 1768 AN: 2110

Alfa AF: 0.815 Hom.: 82639

Bravo AF: 0.860

Asia WGS AF: 0.956 AC: 3324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.12
PhyloP100		0.052
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: rs1556562; hg19: chr1-93034023;