chr19-15226974-C-A

Variant names:

• chr19-15226974-C-A
• rs757291
• NM_024794.3:c.*463G>T

Variant summary

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

The NM_024794.3(EPHX3):​c.*463G>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: 32)
• Consequence: EPHX3 NM_024794.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 5 publications found

Genes affected

EPHX3 (HGNC:23760): (epoxide hydrolase 3) Enables epoxide hydrolase activity. Involved in epoxide metabolic process. Located in intracellular membrane-bounded organelle and membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHX3	NM_024794.3	c.*463G>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000221730.8	NP_079070.1
EPHX3	NM_001142886.2	c.*463G>T		3_prime_UTR_variant	Exon 8 of 8		NP_001136358.1
EPHX3	XM_024451725.2	c.*463G>T		3_prime_UTR_variant	Exon 9 of 9		XP_024307493.1
EPHX3	XM_047439452.1	c.*463G>T		3_prime_UTR_variant	Exon 9 of 9		XP_047295408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHX3	ENST00000221730.8	c.*463G>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_024794.3	ENSP00000221730.2
EPHX3	ENST00000435261.5	c.*463G>T		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000410323.1
EPHX3	ENST00000602233.5	c.*463G>T		3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000469345.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.69
DANN	Benign	0.42
PhyloP100		-0.055

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: rs757291; hg19: chr19-15337785;