dbSNP rs2271690: SAR1A:c.58+23C>T (chr10-70161835-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.58+23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,611,708 control chromosomes in the GnomAD database, including 87,549 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 0.27 ( 6478 hom., cov: 32)

Exomes 𝑓: 0.33 ( 81071 hom. )

Consequence

SAR1A
NM_020150.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390

Publications

23 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAR1A	NM_020150.5 link	c.58+23C>T		intron_variant	Intron 2 of 6	ENST00000373241.9	NP_064535.1
SAR1A	NM_001142648.2 link	c.58+23C>T		intron_variant	Intron 3 of 7		NP_001136120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAR1A	ENST00000373241.9 link	c.58+23C>T		intron_variant	Intron 2 of 6	1	NM_020150.5	ENSP00000362338.4

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40411

AN:

151972

Hom.:

6470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0837

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.299

GnomAD2 exomes

AF:

0.320

AC:

80409

AN:

251226

AF XY:

0.314

show subpopulations

Gnomad AFR exome

AF:

0.0746

Gnomad AMR exome

AF:

0.472

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.436

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.324

Gnomad OTH exome

AF:

0.329

GnomAD4 exome

AF:

0.327

AC:

476599

AN:

1459618

Hom.:

81071

Cov.:

AF XY:

0.324

AC XY:

235179

AN XY:

726232

show subpopulations

African (AFR)

AF:

0.0691

AC:

2310

AN:

33448

American (AMR)

AF:

0.460

AC:

20572

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

8976

AN:

26124

East Asian (EAS)

AF:

0.430

AC:

17076

AN:

39670

South Asian (SAS)

AF:

0.237

AC:

20447

AN:

86204

European-Finnish (FIN)

AF:

0.250

AC:

13346

AN:

53410

Middle Eastern (MID)

AF:

0.271

AC:

1531

AN:

5640

European-Non Finnish (NFE)

AF:

0.336

AC:

373048

AN:

1110124

Other (OTH)

AF:

0.320

AC:

19293

AN:

60300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

15343

30687

46030

61374

76717

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12104

24208

36312

48416

60520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.266

AC:

40422

AN:

152090

Hom.:

6478

Cov.:

AF XY:

0.265

AC XY:

19690

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.0835

AC:

3466

AN:

41494

American (AMR)

AF:

0.398

AC:

6085

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

1179

AN:

3468

East Asian (EAS)

AF:

0.432

AC:

2235

AN:

5176

South Asian (SAS)

AF:

0.232

AC:

1122

AN:

4826

European-Finnish (FIN)

AF:

0.246

AC:

2596

AN:

10568

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.332

AC:

22553

AN:

67954

Other (OTH)

AF:

0.298

AC:

628

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1448

2896

4343

5791

7239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.310

Hom.:

19372

Bravo

AF:

0.277

Asia WGS

AF:

0.313

AC:

1088

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.96

(source)

DANN

Benign

0.35

PhyloP100

-0.039

PromoterAI

-0.038

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over