chr1-92689790-C-T

Variant names:

• chr1-92689790-C-T
• rs4847267
• NM_001350197.2:c.1097+4012G>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.1097+4012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,064 control chromosomes in the GnomAD database, including 29,380 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 0.61 (29380 hom., cov: 33)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.1097+4012G>A		intron_variant	Intron 9 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.1097+4012G>A		intron_variant	Intron 9 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93134 AN: 151946 Hom.: 29376 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.613 AC: 93177 AN: 152064 Hom.: 29380 Cov.: 33 AF XY: 0.617 AC XY: 45891 AN XY: 74336

African (AFR) AF: 0.490 AC: 20310 AN: 41434

American (AMR) AF: 0.654 AC: 9987 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2378 AN: 3472

East Asian (EAS) AF: 0.917 AC: 4760 AN: 5192

South Asian (SAS) AF: 0.787 AC: 3797 AN: 4826

European-Finnish (FIN) AF: 0.627 AC: 6630 AN: 10570

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43223 AN: 67984

Other (OTH) AF: 0.588 AC: 1244 AN: 2114

Alfa AF: 0.631 Hom.: 4661

Bravo AF: 0.609

Asia WGS AF: 0.797 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		0.28
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: rs4847267; hg19: chr1-93155347;