rs10865879

Variant names:

• chr3-38535871-A-C
• rs10865879
• ENST00000474071.5:n.1405-5896A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000474071.5(EXOG):​n.1405-5896A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,204 control chromosomes in the GnomAD database, including 3,494 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 (3494 hom., cov: 33)
• Consequence: EXOG ENST00000474071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

EXOG (HGNC:3347): (exo/endonuclease G) This gene encodes an endo/exonuclease with 5'-3' exonuclease activity. The encoded enzyme catalyzes the hydrolysis of ester linkages at the 5' end of a nucleic acid chain. This enzyme is localized to the mitochondria and may play a role in programmed cell death. Alternatively spliced transcript variants have been described. A pseudogene exists on chromosome 18. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOG	ENST00000474071.5	n.1405-5896A>C		intron_variant	Intron 6 of 6	2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32207 AN: 152084 Hom.: 3491 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.212 AC: 32223 AN: 152204 Hom.: 3494 Cov.: 33 AF XY: 0.211 AC XY: 15729 AN XY: 74410

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.206

Alfa AF: 0.218 Hom.: 520

Bravo AF: 0.206

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10865879; hg19: chr3-38577362;