Variant rs5030754 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_004446.3(EPRS1):c.3102G>A(p.Lys1034=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.09 in 1,605,802 control chromosomes in the GnomAD database, including 7,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1366 hom., cov: 33)

Exomes 𝑓: 0.087 ( 6328 hom. )

Consequence

EPRS1
NM_004446.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.05

Variant links:

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]

EPRS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BP6

Variant 1-219983387-C-T is Benign according to our data. Variant chr1-219983387-C-T is described in ClinVar as [Benign]. Clinvar id is 1166607.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPRS1	NM_004446.3 linkuse as main transcript	c.3102G>A	p.Lys1034=	synonymous_variant	22/32	ENST00000366923.8	NP_004437.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPRS1	ENST00000366923.8 linkuse as main transcript	c.3102G>A	p.Lys1034=	synonymous_variant	22/32	1	NM_004446.3	ENSP00000355890	P1
EPRS1	ENST00000485821.1 linkuse as main transcript	n.65G>A		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18031

AN:

152130

Hom.:

1365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.0767

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.0625

Gnomad SAS

AF:

0.0410

Gnomad FIN

AF:

0.0619

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0922

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0798

AC:

19772

AN:

247864

Hom.:

1014

AF XY:

0.0765

AC XY:

10240

AN XY:

133838

show subpopulations

Gnomad AFR exome

AF:

0.219

Gnomad AMR exome

AF:

0.0493

Gnomad ASJ exome

AF:

0.0315

Gnomad EAS exome

AF:

0.0637

Gnomad SAS exome

AF:

0.0336

Gnomad FIN exome

AF:

0.0675

Gnomad NFE exome

AF:

0.0903

Gnomad OTH exome

AF:

0.0816

GnomAD4 exome

AF:

0.0870

AC:

126456

AN:

1453554

Hom.:

6328

Cov.:

AF XY:

0.0849

AC XY:

61384

AN XY:

723168

show subpopulations

Gnomad4 AFR exome

AF:

0.229

Gnomad4 AMR exome

AF:

0.0542

Gnomad4 ASJ exome

AF:

0.0324

Gnomad4 EAS exome

AF:

0.0602

Gnomad4 SAS exome

AF:

0.0349

Gnomad4 FIN exome

AF:

0.0721

Gnomad4 NFE exome

AF:

0.0911

Gnomad4 OTH exome

AF:

0.0886

GnomAD4 genome

AF:

0.119

AC:

18066

AN:

152248

Hom.:

1366

Cov.:

AF XY:

0.113

AC XY:

8415

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.0766

Gnomad4 ASJ

AF:

0.0334

Gnomad4 EAS

AF:

0.0628

Gnomad4 SAS

AF:

0.0414

Gnomad4 FIN

AF:

0.0619

Gnomad4 NFE

AF:

0.0922

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.102

Hom.:

465

Bravo

AF:

0.125

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

EpiCase

AF:

0.0916

EpiControl

AF:

0.0867

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

6.7

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over