Genetic Variant SAR1A:c.-91C>A (chr10-70170487-G-T) – 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.-91C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 152,726 control chromosomes in the GnomAD database, including 108 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 0.026 ( 107 hom., cov: 30)

Exomes 𝑓: 0.032 ( 1 hom. )

Consequence

SAR1A
NM_020150.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.34

Publications

4 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:

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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=-0.63).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020150.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	NM_020150.5	MANE Select	c.-91C>A		5_prime_UTR	Exon 1 of 7	NP_064535.1	Q9NR31-1
	SAR1A	NM_001142648.2		c.-161C>A		5_prime_UTR	Exon 1 of 8	NP_001136120.1	Q9NR31-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SAR1A	ENST00000373241.9	TSL:1 MANE Select	c.-91C>A	5_prime_UTR	Exon 1 of 7	ENSP00000362338.4	Q9NR31-1
SAR1A	ENST00000373242.6	TSL:2	c.-161C>A	5_prime_UTR	Exon 1 of 8	ENSP00000362339.1	Q9NR31-1
SAR1A	ENST00000870136.1		c.-87C>A	5_prime_UTR	Exon 1 of 7	ENSP00000540195.1

Frequencies

GnomAD3 genomes

AF:

0.0261

AC:

3959

AN:

151960

Hom.:

107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0307

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.0376

Gnomad FIN

AF:

0.00972

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0175

Gnomad OTH

AF:

0.0244

GnomAD4 exome

AF:

0.0324

AC:

AN:

648

Hom.:

Cov.:

AF XY:

0.0300

AC XY:

AN XY:

500

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.179

AC:

AN:

South Asian (SAS)

AF:

0.0625

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0264

AC:

AN:

530

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0260

AC:

3956

AN:

152078

Hom.:

107

Cov.:

AF XY:

0.0270

AC XY:

2003

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0306

AC:

1271

AN:

41514

American (AMR)

AF:

0.0222

AC:

339

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3470

East Asian (EAS)

AF:

0.146

AC:

751

AN:

5136

South Asian (SAS)

AF:

0.0376

AC:

181

AN:

4814

European-Finnish (FIN)

AF:

0.00972

AC:

103

AN:

10602

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0175

AC:

1186

AN:

67954

Other (OTH)

AF:

0.0246

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

193

385

578

770

963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0168

Hom.:

Bravo

AF:

0.0272

Asia WGS

AF:

0.0870

AC:

302

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.089

(source)

DANN

Benign

0.93

PhyloP100

-3.3

PromoterAI

-0.089

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over