Genetic Variant SAR1A:c.-17+100T>G (chr10-70170313-A-C) – 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.-17+100T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 91,048 control chromosomes in the GnomAD database, including 29,435 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 0.82 ( 29435 hom., cov: 11)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

SAR1A
NM_020150.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167

Publications

7 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=-0.56).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAR1A	NM_020150.5 link	c.-17+100T>G		intron_variant	Intron 1 of 6	ENST00000373241.9	NP_064535.1	Q9NR31-1Q5SQT9
SAR1A	NM_001142648.2 link	c.-87+100T>G		intron_variant	Intron 1 of 7		NP_001136120.1	Q9NR31-1Q5SQT9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SAR1A	ENST00000373241.9 link	c.-17+100T>G	intron_variant	Intron 1 of 6	1	NM_020150.5	ENSP00000362338.4	Q9NR31-1
SAR1A	ENST00000373242.6 link	c.-87+100T>G	intron_variant	Intron 1 of 7	2		ENSP00000362339.1	Q9NR31-1
SAR1A	ENST00000373239.2 link	c.-217+100T>G	intron_variant	Intron 1 of 4	3		ENSP00000362336.2	X1WI22

Frequencies

GnomAD3 genomes

AF:

0.823

AC:

74880

AN:

91024

Hom.:

29437

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.892

Gnomad AMR

AF:

0.824

Gnomad ASJ

AF:

0.796

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.838

Gnomad FIN

AF:

0.847

Gnomad MID

AF:

0.874

Gnomad NFE

AF:

0.882

Gnomad OTH

AF:

0.822

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.823

AC:

74891

AN:

91046

Hom.:

29435

Cov.:

AF XY:

0.818

AC XY:

34993

AN XY:

42790

show subpopulations

African (AFR)

AF:

0.675

AC:

12214

AN:

18096

American (AMR)

AF:

0.824

AC:

7500

AN:

9102

Ashkenazi Jewish (ASJ)

AF:

0.796

AC:

2030

AN:

2550

East Asian (EAS)

AF:

0.671

AC:

1774

AN:

2644

South Asian (SAS)

AF:

0.840

AC:

2183

AN:

2600

European-Finnish (FIN)

AF:

0.847

AC:

4218

AN:

4982

Middle Eastern (MID)

AF:

0.876

AC:

177

AN:

202

European-Non Finnish (NFE)

AF:

0.882

AC:

43274

AN:

49068

Other (OTH)

AF:

0.820

AC:

977

AN:

1192

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

602

1205

1807

2410

3012

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

-0.17

PromoterAI

0.0014

Neutral

(source)

Mutation Taster

=84/16

polymorphism

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over