Variant 5-134606802-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000439578.5(SAR1B):c.*148A>G variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 682,524 control chromosomes in the GnomAD database, including 9,813 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2055 hom., cov: 32)

Exomes 𝑓: 0.15 ( 7758 hom. )

Consequence

SAR1B
ENST00000439578.5 splice_region

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.623

Variant links:

Genes affected

SAR1B (HGNC:10535): (secretion associated Ras related GTPase 1B) The protein encoded by this gene is a small GTPase that acts as a homodimer. The encoded protein is activated by the guanine nucleotide exchange factor PREB and is involved in protein transport from the endoplasmic reticulum to the Golgi. This protein is part of the COPII coat complex. Defects in this gene are a cause of chylomicron retention disease (CMRD), also known as Anderson disease (ANDD). Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Mar 2010]

SAR1B links:

SAR1B (HGNC:):

SAR1B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 5-134606802-T-C is Benign according to our data. Variant chr5-134606802-T-C is described in ClinVar as [Benign]. Clinvar id is 1247459.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-134606802-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
SAR1B	NM_016103.4 linkuse as main transcript	c.*148A>G	3_prime_UTR_variant	7/7	ENST00000402673.7	NP_057187.1	Q9Y6B6
SAR1B	NM_001033503.3 linkuse as main transcript	c.*148A>G	3_prime_UTR_variant	8/8		NP_001028675.1	Q9Y6B6
SAR1B	XM_047417257.1 linkuse as main transcript	c.*148A>G	3_prime_UTR_variant	7/7		XP_047273213.1
SAR1B	XM_047417258.1 linkuse as main transcript	c.*148A>G	3_prime_UTR_variant	5/5		XP_047273214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAR1B	ENST00000402673 linkuse as main transcript	c.*148A>G		3_prime_UTR_variant	7/7	1	NM_016103.4	ENSP00000385432.2		Q9Y6B6

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23863

AN:

152090

Hom.:

2046

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0780

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.152

GnomAD4 exome

AF:

0.155

AC:

81996

AN:

530316

Hom.:

7758

Cov.:

AF XY:

0.153

AC XY:

44073

AN XY:

288532

show subpopulations

Gnomad4 AFR exome

AF:

0.179

Gnomad4 AMR exome

AF:

0.285

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.355

Gnomad4 SAS exome

AF:

0.174

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.142

GnomAD4 genome

AF:

0.157

AC:

23895

AN:

152208

Hom.:

2055

Cov.:

AF XY:

0.161

AC XY:

11953

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.317

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.154

Alfa

AF:

0.126

Hom.:

2424

Bravo

AF:

0.164

Asia WGS

AF:

0.253

AC:

877

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.85

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