dbSNP rs3812692: SAR1A:c.-50C>T (chr10-70170446-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020150.5(SAR1A):c.-50C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 152,026 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.016 ( 69 hom., cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SAR1A
NM_020150.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.537

Publications

3 publications found

Variant links:

Genes affected

SAR1A (HGNC:10534): (secretion associated Ras related GTPase 1A) Predicted to enable GTPase activity. Involved in COPII-coated vesicle cargo loading. Part of COPII vesicle coat. [provided by Alliance of Genome Resources, Apr 2022]

SAR1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAR1A	NM_020150.5 link	c.-50C>T		5_prime_UTR_variant	Exon 1 of 7	ENST00000373241.9	NP_064535.1	Q9NR31-1Q5SQT9
SAR1A	NM_001142648.2 link	c.-120C>T		5_prime_UTR_variant	Exon 1 of 8		NP_001136120.1	Q9NR31-1Q5SQT9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SAR1A	ENST00000373241.9 link	c.-50C>T	5_prime_UTR_variant	Exon 1 of 7	1	NM_020150.5	ENSP00000362338.4	Q9NR31-1
SAR1A	ENST00000373242.6 link	c.-120C>T	5_prime_UTR_variant	Exon 1 of 8	2		ENSP00000362339.1	Q9NR31-1
SAR1A	ENST00000373239.2 link	c.-250C>T	5_prime_UTR_variant	Exon 1 of 5	3		ENSP00000362336.2	X1WI22

Frequencies

GnomAD3 genomes

AF:

0.0156

AC:

2374

AN:

151908

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00324

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0716

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.0807

Gnomad SAS

AF:

0.00560

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00902

Gnomad OTH

AF:

0.0192

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

154

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

124

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

120

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

AF:

0.0156

AC:

2374

AN:

152026

Hom.:

Cov.:

AF XY:

0.0171

AC XY:

1270

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.00323

AC:

134

AN:

41500

American (AMR)

AF:

0.0718

AC:

1096

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3470

East Asian (EAS)

AF:

0.0801

AC:

411

AN:

5130

South Asian (SAS)

AF:

0.00561

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.00189

AC:

AN:

10582

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00902

AC:

613

AN:

67950

Other (OTH)

AF:

0.0190

AC:

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

107

213

320

426

533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0245

Hom.:

Bravo

AF:

0.0233

Asia WGS

AF:

0.0330

AC:

115

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.5

(source)

DANN

Benign

0.72

PhyloP100

-0.54

PromoterAI

0.0040

Neutral

(source)

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.2

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over