1-92655550-G-C

Variant names:

• chr1-92655550-G-C
• rs10735781
• NM_001350197.2:c.1392+7169C>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.1392+7169C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,862 control chromosomes in the GnomAD database, including 26,989 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 0.58 (26989 hom., cov: 31)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 16 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 = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.1392+7169C>G		intron_variant	Intron 13 of 19	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2	c.1392+7169C>G		intron_variant	Intron 13 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87489 AN: 151744 Hom.: 26991 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.576 AC: 87499 AN: 151862 Hom.: 26989 Cov.: 31 AF XY: 0.582 AC XY: 43154 AN XY: 74208

African (AFR) AF: 0.359 AC: 14879 AN: 41422

American (AMR) AF: 0.638 AC: 9736 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3468

East Asian (EAS) AF: 0.926 AC: 4792 AN: 5174

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6600 AN: 10504

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43283 AN: 67906

Other (OTH) AF: 0.561 AC: 1181 AN: 2104

Alfa AF: 0.605 Hom.: 3614

Bravo AF: 0.568

Asia WGS AF: 0.795 AC: 2761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.46
PhyloP100		-0.81
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: rs10735781; hg19: chr1-93121107;