1-220015094-A-G

Variant names:

• chr1-220015094-A-G
• rs10779396
• NM_004446.3:c.1494+3355T>C

Variant summary

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

The NM_004446.3(EPRS1):​c.1494+3355T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,196 control chromosomes in the GnomAD database, including 49,723 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 0.81 (49723 hom., cov: 32)
• Consequence: EPRS1 NM_004446.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

EPRS1 (HGNC:3418): (glutamyl-prolyl-tRNA synthetase 1) Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. The protein encoded by this gene is a multifunctional aminoacyl-tRNA synthetase that catalyzes the aminoacylation of glutamic acid and proline tRNA species. Alternative splicing has been observed for this gene, but the full-length nature and biological validity of the variant have not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPRS1	NM_004446.3	c.1494+3355T>C		intron_variant	Intron 12 of 31	ENST00000366923.8	NP_004437.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPRS1	ENST00000366923.8	c.1494+3355T>C		intron_variant	Intron 12 of 31	1	NM_004446.3	ENSP00000355890.3
EPRS1	ENST00000609181.5	c.1515+3032T>C		intron_variant	Intron 13 of 20	1		ENSP00000477245.1
EPRS1	ENST00000477030.2	n.*520+3901T>C		intron_variant	Intron 9 of 11	1		ENSP00000477493.1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122757 AN: 152078 Hom.: 49684 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.798

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.807 AC: 122849 AN: 152196 Hom.: 49723 Cov.: 32 AF XY: 0.808 AC XY: 60153 AN XY: 74412

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.799

Alfa AF: 0.815 Hom.: 8184

Bravo AF: 0.807

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.087
DANN	Benign	0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs10779396; hg19: chr1-220188436;