Variant 1-109235955-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.970-22T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 1,585,244 control chromosomes in the GnomAD database, including 483,445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 39737 hom., cov: 31)

Exomes 𝑓: 0.78 ( 443708 hom. )

Consequence

SARS1
NM_006513.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.783

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 (BayesDel_noAF=-0.81).

BP6

Variant 1-109235955-T-C is Benign according to our data. Variant chr1-109235955-T-C is described in ClinVar as [Benign]. Clinvar id is 1327979.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.970-22T>C		intron_variant		ENST00000234677.7	NP_006504.2	P49591Q0VGA5
SARS1	NM_001330669.1 linkuse as main transcript	c.970-22T>C		intron_variant			NP_001317598.1	Q5T5C7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SARS1	ENST00000234677.7 linkuse as main transcript	c.970-22T>C		intron_variant		1	NM_006513.4	ENSP00000234677.2		P49591
SARS1	ENST00000369923.4 linkuse as main transcript	c.970-22T>C		intron_variant		5		ENSP00000358939.4		Q5T5C7

Frequencies

GnomAD3 genomes

AF:

0.710

AC:

107866

AN:

151944

Hom.:

39725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.498

Gnomad AMI

AF:

0.741

Gnomad AMR

AF:

0.786

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:

0.753

GnomAD3 exomes

AF:

0.769

AC:

175087

AN:

227618

Hom.:

68480

AF XY:

0.768

AC XY:

94435

AN XY:

122892

show subpopulations

Gnomad AFR exome

AF:

0.487

Gnomad AMR exome

AF:

0.814

Gnomad ASJ exome

AF:

0.853

Gnomad EAS exome

AF:

0.899

Gnomad SAS exome

AF:

0.659

Gnomad FIN exome

AF:

0.776

Gnomad NFE exome

AF:

0.796

Gnomad OTH exome

AF:

0.784

GnomAD4 exome

AF:

0.784

AC:

1123335

AN:

1433182

Hom.:

443708

Cov.:

AF XY:

0.781

AC XY:

556665

AN XY:

712394

show subpopulations

Gnomad4 AFR exome

AF:

0.480

Gnomad4 AMR exome

AF:

0.811

Gnomad4 ASJ exome

AF:

0.856

Gnomad4 EAS exome

AF:

0.884

Gnomad4 SAS exome

AF:

0.662

Gnomad4 FIN exome

AF:

0.774

Gnomad4 NFE exome

AF:

0.797

Gnomad4 OTH exome

AF:

0.777

GnomAD4 genome

AF:

0.710

AC:

107917

AN:

152062

Hom.:

39737

Cov.:

AF XY:

0.708

AC XY:

52618

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.498

Gnomad4 AMR

AF:

0.786

Gnomad4 ASJ

AF:

0.871

Gnomad4 EAS

AF:

0.893

Gnomad4 SAS

AF:

0.668

Gnomad4 FIN

AF:

0.765

Gnomad4 NFE

AF:

0.792

Gnomad4 OTH

AF:

0.755

Alfa

AF:

0.753

Hom.:

8767

Bravo

AF:

0.706

Asia WGS

AF:

0.758

AC:

2634

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

-0.81

CADD

Benign

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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