3-38524989-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005107.4(EXOG):​c.*627G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: EXOG NM_005107.4 3_prime_UTR
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005107.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOG	NM_005107.4	MANE Select	c.*627G>T		3_prime_UTR	Exon 6 of 6	NP_005098.2	Q9Y2C4-1
	EXOG	NM_001145464.2		c.*627G>T		3_prime_UTR	Exon 5 of 5	NP_001138936.1	Q9Y2C4-4
	EXOG	NR_134938.2		n.1592G>T		non_coding_transcript_exon	Exon 8 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOG	ENST00000287675.10	TSL:1 MANE Select	c.*627G>T		3_prime_UTR	Exon 6 of 6	ENSP00000287675.5	Q9Y2C4-1
	EXOG	ENST00000457367.5	TSL:1	n.*1508G>T		non_coding_transcript_exon	Exon 9 of 9	ENSP00000402164.1	F8WE38
	EXOG	ENST00000457367.5	TSL:1	n.*1508G>T		3_prime_UTR	Exon 9 of 9	ENSP00000402164.1	F8WE38

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 2702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0090
DANN	Benign	0.44
PhyloP100		-2.1

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;