1-92573954-T-C

Variant names:

• chr1-92573954-T-C
• rs2391164
• NM_001350197.2:c.2071-10217A>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.2071-10217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,122 control chromosomes in the GnomAD database, including 64,638 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 0.92 (64638 hom., cov: 31)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• 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=-0.94).
• 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.2071-10217A>G		intron	N/A	NP_001337126.1
	EVI5	NM_001308248.2		c.2056-10217A>G		intron	N/A	NP_001295177.1
	EVI5	NM_001377210.1		c.2047-10217A>G		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.2071-10217A>G		intron	N/A	ENSP00000506999.1
	EVI5	ENST00000540033.3	TSL:1	c.2056-10217A>G		intron	N/A	ENSP00000440826.2
	EVI5	ENST00000370331.5	TSL:1	c.2023-10217A>G		intron	N/A	ENSP00000359356.1

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140023 AN: 152004 Hom.: 64587 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.921 AC: 140134 AN: 152122 Hom.: 64638 Cov.: 31 AF XY: 0.922 AC XY: 68593 AN XY: 74358

African (AFR) AF: 0.946 AC: 39266 AN: 41520

American (AMR) AF: 0.934 AC: 14259 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3329 AN: 3472

East Asian (EAS) AF: 0.968 AC: 5026 AN: 5190

South Asian (SAS) AF: 0.967 AC: 4663 AN: 4822

European-Finnish (FIN) AF: 0.884 AC: 9362 AN: 10590

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61158 AN: 67938

Other (OTH) AF: 0.912 AC: 1927 AN: 2114

Alfa AF: 0.915 Hom.: 10609

Bravo AF: 0.924

Asia WGS AF: 0.964 AC: 3350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.53
PhyloP100		-1.1
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: rs2391164; hg19: chr1-93039511;