1-109236451-G-A

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_006513.4(SARS1):c.1160G>A(p.Gly387Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0117 in 1,604,458 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0089 ( 15 hom., cov: 32)

Exomes 𝑓: 0.012 ( 143 hom. )

Consequence

SARS1
NM_006513.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.58

Variant links:

Genes affected

SARS1 (HGNC:10537): (seryl-tRNA synthetase 1) This gene belongs to the class II amino-acyl tRNA family. The encoded enzyme catalyzes the transfer of L-serine to tRNA (Ser) and is related to bacterial and yeast counterparts. Multiple alternatively spliced transcript variants have been described but the biological validity of all variants is unknown. [provided by RefSeq, Jul 2010]

SARS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009588867).

BP6

Variant 1-109236451-G-A is Benign according to our data. Variant chr1-109236451-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 774395.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00892 (1358/152214) while in subpopulation NFE AF= 0.0142 (963/68018). AF 95% confidence interval is 0.0134. There are 15 homozygotes in gnomad4. There are 636 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SARS1	NM_006513.4 link	c.1160G>A	p.Gly387Glu	missense_variant	Exon 9 of 11	ENST00000234677.7	NP_006504.2	P49591Q0VGA5
SARS1	NM_001330669.1 link	c.1160G>A	p.Gly387Glu	missense_variant	Exon 9 of 12		NP_001317598.1	Q5T5C7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SARS1	ENST00000234677.7 link	c.1160G>A	p.Gly387Glu	missense_variant	Exon 9 of 11	1	NM_006513.4	ENSP00000234677.2	P49591
SARS1	ENST00000369923.4 link	c.1160G>A	p.Gly387Glu	missense_variant	Exon 9 of 12	5		ENSP00000358939.4	Q5T5C7
SARS1	ENST00000468588.1 link	n.221G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.00893

AC:

1358

AN:

152096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00307

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.00885

Gnomad ASJ

AF:

0.0213

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00170

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0142

Gnomad OTH

AF:

0.00908

GnomAD3 exomes

AF:

0.00892

AC:

2243

AN:

251456

Hom.:

AF XY:

0.00868

AC XY:

1180

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.00308

Gnomad AMR exome

AF:

0.00535

Gnomad ASJ exome

AF:

0.0230

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00327

Gnomad FIN exome

AF:

0.00189

Gnomad NFE exome

AF:

0.0138

Gnomad OTH exome

AF:

0.0109

GnomAD4 exome

AF:

0.0120

AC:

17368

AN:

1452244

Hom.:

143

Cov.:

AF XY:

0.0116

AC XY:

8377

AN XY:

720070

show subpopulations

Gnomad4 AFR exome

AF:

0.00276

Gnomad4 AMR exome

AF:

0.00541

Gnomad4 ASJ exome

AF:

0.0237

Gnomad4 EAS exome

AF:

0.0000762

Gnomad4 SAS exome

AF:

0.00343

Gnomad4 FIN exome

AF:

0.00305

Gnomad4 NFE exome

AF:

0.0138

Gnomad4 OTH exome

AF:

0.0114

GnomAD4 genome

AF:

0.00892

AC:

1358

AN:

152214

Hom.:

Cov.:

AF XY:

0.00855

AC XY:

636

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.00306

Gnomad4 AMR

AF:

0.00884

Gnomad4 ASJ

AF:

0.0213

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00170

Gnomad4 NFE

AF:

0.0142

Gnomad4 OTH

AF:

0.00899

Alfa

AF:

0.0136

Hom.:

Bravo

AF:

0.00940

TwinsUK

AF:

0.0154

AC:

ALSPAC

AF:

0.0138

AC:

ESP6500AA

AF:

0.00318

AC:

ESP6500EA

AF:

0.0177

AC:

152

ExAC

AF:

0.00937

AC:

1137

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0149

EpiControl

AF:

0.0147

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SARS1: PP2, BS1, BS2 -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Hyperuricemia, pulmonary hypertension, renal failure, alkalosis syndrome

Benign:1

Sep 27, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.28

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.75

D;.

Eigen

Benign

0.11

Eigen_PC

Uncertain

0.29

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.97

D;D

MetaRNN

Benign

0.0096

T;T

MetaSVM

Benign

-0.71

MutationAssessor

Benign

1.4

L;.

PrimateAI

Pathogenic

0.86

PROVEAN

Pathogenic

-6.0

D;D

REVEL

Uncertain

0.32

Sift

Benign

0.069

T;T

Sift4G

Benign

0.16

T;T

Polyphen

0.18

B;B

Vest4

0.53

MVP

0.50

MPC

1.8

ClinPred

0.030

GERP RS

6.1

Varity_R

0.46

gMVP

0.80

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

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