rs1065800

Variant names:

• chr3-38524989-G-A
• rs1065800
• NM_005107.4:c.*627G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-38524989-G-A
• chr3-38524989-G-T

Variant summary

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

The NM_005107.4(EXOG):​c.*627G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 984,500 control chromosomes in the GnomAD database, including 112,290 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 0.57 (27346 hom., cov: 33)
  • Exomes 𝑓: 0.45 (84944 hom.)
• Consequence: EXOG NM_005107.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOG	NM_005107.4	c.*627G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000287675.10	NP_005098.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOG	ENST00000287675.10	c.*627G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_005107.4	ENSP00000287675.5

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87066 AN: 151950 Hom.: 27292 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.552

GnomAD4 exome AF: 0.447 AC: 371694 AN: 832432 Hom.: 84944 Cov.: 29 AF XY: 0.445 AC XY: 171200 AN XY: 384430

Gnomad4 AFR exome AF: 0.857

Gnomad4 AMR exome AF: 0.604

Gnomad4 ASJ exome AF: 0.520

Gnomad4 EAS exome AF: 0.740

Gnomad4 SAS exome AF: 0.472

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.434

Gnomad4 OTH exome AF: 0.486

GnomAD4 genome AF: 0.573 AC: 87183 AN: 152068 Hom.: 27346 Cov.: 33 AF XY: 0.576 AC XY: 42810 AN XY: 74316

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.552

Alfa AF: 0.432 Hom.: 2423

Bravo AF: 0.600

Asia WGS AF: 0.602 AC: 2095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.41

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: rs1065800; hg19: chr3-38566480;