chr1-92546015-A-G

Variant names:

• chr1-92546015-A-G
• rs6603984
• NM_001350197.2:c.2166+17627T>C

Variant summary

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

The NM_001350197.2(EVI5):​c.2166+17627T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 151,958 control chromosomes in the GnomAD database, including 56,873 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 0.86 (56873 hom., cov: 29)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.2166+17627T>C		intron_variant	Intron 19 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.2166+17627T>C		intron_variant	Intron 19 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130779 AN: 151838 Hom.: 56809 Cov.: 29

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.861 AC: 130906 AN: 151958 Hom.: 56873 Cov.: 29 AF XY: 0.864 AC XY: 64121 AN XY: 74252

African (AFR) AF: 0.959 AC: 39792 AN: 41484

American (AMR) AF: 0.876 AC: 13357 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3079 AN: 3470

East Asian (EAS) AF: 0.969 AC: 4991 AN: 5152

South Asian (SAS) AF: 0.952 AC: 4585 AN: 4814

European-Finnish (FIN) AF: 0.765 AC: 8030 AN: 10490

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54288 AN: 67986

Other (OTH) AF: 0.850 AC: 1788 AN: 2104

Alfa AF: 0.843 Hom.: 6650

Bravo AF: 0.871

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.25
PhyloP100		-0.26
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: rs6603984; hg19: chr1-93011572;