rs11804321

Variant names:

• chr1-92543756-T-C
• rs11804321
• NM_001350197.2:c.2166+19886A>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.2166+19886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,150 control chromosomes in the GnomAD database, including 1,418 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 0.13 (1418 hom., cov: 32)
• Consequence: EVI5 NM_001350197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 9 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 (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2	c.2166+19886A>G		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+19886A>G		intron_variant	Intron 19 of 19		NM_001350197.2	ENSP00000506999.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19262 AN: 152032 Hom.: 1417 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.127 AC: 19282 AN: 152150 Hom.: 1418 Cov.: 32 AF XY: 0.127 AC XY: 9419 AN XY: 74358

African (AFR) AF: 0.0764 AC: 3172 AN: 41504

American (AMR) AF: 0.159 AC: 2427 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3468

East Asian (EAS) AF: 0.0239 AC: 124 AN: 5180

South Asian (SAS) AF: 0.104 AC: 503 AN: 4826

European-Finnish (FIN) AF: 0.138 AC: 1462 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10433 AN: 67994

Other (OTH) AF: 0.159 AC: 335 AN: 2112

Alfa AF: 0.145 Hom.: 6381

Bravo AF: 0.124

Asia WGS AF: 0.0740 AC: 258 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	0.43
DANN	Benign	0.71
PhyloP100		0.45
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: rs11804321; hg19: chr1-93009313;