rs6692187

Variant names:

• chr1-92569463-C-T
• rs6692187
• NM_001350197.2:c.2071-5726G>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.2071-5726G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,206 control chromosomes in the GnomAD database, including 55,224 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 (55224 hom., cov: 31)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.2071-5726G>A		intron_variant	Intron 18 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.2071-5726G>A		intron_variant	Intron 18 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129144 AN: 152088 Hom.: 55177 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.888

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: 0.849 AC: 129249 AN: 152206 Hom.: 55224 Cov.: 31 AF XY: 0.851 AC XY: 63345 AN XY: 74400

African (AFR) AF: 0.918 AC: 38129 AN: 41544

American (AMR) AF: 0.869 AC: 13276 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3079 AN: 3468

East Asian (EAS) AF: 0.968 AC: 5021 AN: 5188

South Asian (SAS) AF: 0.952 AC: 4591 AN: 4824

European-Finnish (FIN) AF: 0.766 AC: 8104 AN: 10574

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

European-Non Finnish (NFE) AF: 0.798 AC: 54282 AN: 68006

Other (OTH) AF: 0.838 AC: 1769 AN: 2112

Alfa AF: 0.842 Hom.: 9461

Bravo AF: 0.857

Asia WGS AF: 0.954 AC: 3318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.088
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: rs6692187; hg19: chr1-93035020;