rs10494092

Positions:

• chr1-108591217-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001010883.3(EEIG2):​c.138-9349A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,234 control chromosomes in the GnomAD database, including 4,443 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 0.21 (4443 hom., cov: 32)
• Consequence: EEIG2 NM_001010883.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

Genes affected

EEIG2 (HGNC:27637): (EEIG family member 2)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEIG2	NM_001010883.3	c.138-9349A>G		intron_variant		ENST00000370035.8	NP_001010883.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEIG2	ENST00000370035.8	c.138-9349A>G		intron_variant		1	NM_001010883.3	ENSP00000359052.3
EEIG2	ENST00000405454.1	c.138-9349A>G		intron_variant		5		ENSP00000386084.1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32601 AN: 152116 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.214 AC: 32590 AN: 152234 Hom.: 4443 Cov.: 32 AF XY: 0.212 AC XY: 15792 AN XY: 74436

Gnomad4 AFR AF: 0.0556

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.207

Alfa AF: 0.285 Hom.: 8838

Bravo AF: 0.203

Asia WGS AF: 0.171 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	16
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494092; hg19: chr1-109133839; COSMIC: COSV64240356;