rs10747448

Variant names:

• chr1-92655773-T-C
• rs10747448
• NM_001350197.2:c.1392+6946A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-92655773-T-C
• chr1-92655773-T-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+6946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,204 control chromosomes in the GnomAD database, including 64,667 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 0.92 (64667 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 7 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=-0.89).
• 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 rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.1392+6946A>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+6946A>G		intron_variant	Intron 13 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140102 AN: 152086 Hom.: 64616 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.921 AC: 140213 AN: 152204 Hom.: 64667 Cov.: 32 AF XY: 0.922 AC XY: 68632 AN XY: 74406

African (AFR) AF: 0.945 AC: 39257 AN: 41538

American (AMR) AF: 0.934 AC: 14292 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3329 AN: 3472

East Asian (EAS) AF: 0.968 AC: 5007 AN: 5170

South Asian (SAS) AF: 0.967 AC: 4666 AN: 4826

European-Finnish (FIN) AF: 0.885 AC: 9357 AN: 10578

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61229 AN: 67996

Other (OTH) AF: 0.913 AC: 1931 AN: 2116

Alfa AF: 0.916 Hom.: 11111

Bravo AF: 0.924

Asia WGS AF: 0.962 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.21
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: rs10747448; hg19: chr1-93121330;