chr3-38535871-A-C

Position:

• chr3-38535871-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXOG	ENST00000474071.5	n.1405-5896A>C		intron_variant, non_coding_transcript_variant		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;