1-92527990-A-C

Position:

• chr1-92527990-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350197.2(EVI5):​c.2167-14020T>G 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 152,190 control chromosomes in the GnomAD database, including 55,594 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 (55594 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.2167-14020T>G		intron_variant		ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.2167-14020T>G		intron_variant			NM_001350197.2	ENSP00000506999	P1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129517 AN: 152072 Hom.: 55538 Cov.: 32

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: 129635 AN: 152190 Hom.: 55594 Cov.: 32 AF XY: 0.854 AC XY: 63559 AN XY: 74408

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.837

Alfa AF: 0.842 Hom.: 10344

Bravo AF: 0.860

Asia WGS AF: 0.955 AC: 3320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970712; hg19: chr1-92993547;