dbSNP rs11438971: SAR1A:c.-330_-329insT (chr10-70171117-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000948610.1(SAR1A):c.-330_-329insT variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.94 ( 66588 hom., cov: 0)

Consequence

SAR1A
ENST00000948610.1 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.691

Publications

2 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000948610.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	ENST00000948610.1		c.-330_-329insT		upstream_gene	N/A	ENSP00000618669.1

Frequencies

GnomAD3 genomes

AF:

0.936

AC:

141981

AN:

151694

Hom.:

66533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.955

Gnomad AMI

AF:

0.988

Gnomad AMR

AF:

0.943

Gnomad ASJ

AF:

0.903

Gnomad EAS

AF:

0.991

Gnomad SAS

AF:

0.904

Gnomad FIN

AF:

0.951

Gnomad MID

AF:

0.858

Gnomad NFE

AF:

0.920

Gnomad OTH

AF:

0.923

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.936

AC:

142095

AN:

151812

Hom.:

66588

Cov.:

AF XY:

0.937

AC XY:

69466

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.955

AC:

39544

AN:

41394

American (AMR)

AF:

0.943

AC:

14391

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.903

AC:

3135

AN:

3470

East Asian (EAS)

AF:

0.991

AC:

5104

AN:

5152

South Asian (SAS)

AF:

0.904

AC:

4336

AN:

4796

European-Finnish (FIN)

AF:

0.951

AC:

9989

AN:

10508

Middle Eastern (MID)

AF:

0.857

AC:

252

AN:

294

European-Non Finnish (NFE)

AF:

0.920

AC:

62495

AN:

67910

Other (OTH)

AF:

0.923

AC:

1948

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

461

921

1382

1842

2303

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<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:

0.929

Hom.:

8006

Bravo

AF:

0.935

Asia WGS

AF:

0.950

AC:

3305

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.69

Splicing

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