Variant 1-109228441-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006513.4(SARS1):c.288+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 1,589,930 control chromosomes in the GnomAD database, including 483,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 39251 hom., cov: 32)

Exomes 𝑓: 0.78 ( 444225 hom. )

Consequence

SARS1
NM_006513.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.623

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:

SARS1 (HGNC:):

SARS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-109228441-T-C is Benign according to our data. Variant chr1-109228441-T-C is described in ClinVar as [Benign]. Clinvar id is 1327978.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SARS1	NM_006513.4 linkuse as main transcript	c.288+9T>C		intron_variant		ENST00000234677.7	NP_006504.2	P49591Q0VGA5
SARS1	NM_001330669.1 linkuse as main transcript	c.288+9T>C		intron_variant			NP_001317598.1	Q5T5C7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SARS1	ENST00000234677.7 linkuse as main transcript	c.288+9T>C	intron_variant	1	NM_006513.4	ENSP00000234677.2	P49591
SARS1	ENST00000369923.4 linkuse as main transcript	c.288+9T>C	intron_variant	5		ENSP00000358939.4	Q5T5C7
SARS1	ENST00000477544.5 linkuse as main transcript	n.313+9T>C	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

106853

AN:

151982

Hom.:

39240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.741

Gnomad AMR

AF:

0.783

Gnomad ASJ

AF:

0.871

Gnomad EAS

AF:

0.894

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.765

Gnomad MID

AF:

0.785

Gnomad NFE

AF:

0.792

Gnomad OTH

AF:

0.750

GnomAD3 exomes

AF:

0.768

AC:

191370

AN:

249204

Hom.:

74816

AF XY:

0.766

AC XY:

103263

AN XY:

134744

show subpopulations

Gnomad AFR exome

AF:

0.463

Gnomad AMR exome

AF:

0.812

Gnomad ASJ exome

AF:

0.857

Gnomad EAS exome

AF:

0.899

Gnomad SAS exome

AF:

0.658

Gnomad FIN exome

AF:

0.776

Gnomad NFE exome

AF:

0.796

Gnomad OTH exome

AF:

0.787

GnomAD4 exome

AF:

0.783

AC:

1125252

AN:

1437830

Hom.:

444225

Cov.:

AF XY:

0.780

AC XY:

559296

AN XY:

716830

show subpopulations

Gnomad4 AFR exome

AF:

0.456

Gnomad4 AMR exome

AF:

0.810

Gnomad4 ASJ exome

AF:

0.857

Gnomad4 EAS exome

AF:

0.884

Gnomad4 SAS exome

AF:

0.662

Gnomad4 FIN exome

AF:

0.773

Gnomad4 NFE exome

AF:

0.796

Gnomad4 OTH exome

AF:

0.775

GnomAD4 genome

AF:

0.703

AC:

106901

AN:

152100

Hom.:

39251

Cov.:

AF XY:

0.702

AC XY:

52158

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.474

Gnomad4 AMR

AF:

0.782

Gnomad4 ASJ

AF:

0.871

Gnomad4 EAS

AF:

0.893

Gnomad4 SAS

AF:

0.667

Gnomad4 FIN

AF:

0.765

Gnomad4 NFE

AF:

0.792

Gnomad4 OTH

AF:

0.753

Alfa

AF:

0.776

Hom.:

78081

Bravo

AF:

0.698

Asia WGS

AF:

0.755

AC:

2624

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Neurodevelopmental disorder with microcephaly, ataxia, and seizures

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.3

DANN

Benign

0.42

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