chr3-38524989-G-A

Variant names:

• chr3-38524989-G-A
• rs1065800
• ENST00000457367.5:n.*1508G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457367.5(EXOG):​n.*1508G>A variant causes a non coding transcript exon 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 ENST00000457367.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.857 AC: 13519 AN: 15776

American (AMR) AF: 0.604 AC: 594 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 2678 AN: 5154

East Asian (EAS) AF: 0.740 AC: 2684 AN: 3628

South Asian (SAS) AF: 0.472 AC: 7759 AN: 16446

European-Finnish (FIN) AF: 0.428 AC: 118 AN: 276

Middle Eastern (MID) AF: 0.515 AC: 834 AN: 1620

European-Non Finnish (NFE) AF: 0.434 AC: 330259 AN: 761260

Other (OTH) AF: 0.486 AC: 13249 AN: 27288

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

African (AFR) AF: 0.821 AC: 34097 AN: 41508

American (AMR) AF: 0.612 AC: 9359 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3468

East Asian (EAS) AF: 0.740 AC: 3826 AN: 5168

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4814

European-Finnish (FIN) AF: 0.466 AC: 4916 AN: 10546

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29056 AN: 67956

Other (OTH) AF: 0.552 AC: 1162 AN: 2104

Alfa AF: 0.446 Hom.: 2702

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
PhyloP100		-2.1
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: rs1065800; hg19: chr3-38566480;