Genetic Variant SAR1A:c.-17+100T>C (chr10-70170313-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020150.5(SAR1A):c.-17+100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00080 ( 0 hom., cov: 11)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAR1A	NM_020150.5 link	c.-17+100T>C		intron_variant	Intron 1 of 6	ENST00000373241.9	NP_064535.1	Q9NR31-1Q5SQT9
SAR1A	NM_001142648.2 link	c.-87+100T>C		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>C	intron_variant	Intron 1 of 6	1	NM_020150.5	ENSP00000362338.4	Q9NR31-1
SAR1A	ENST00000373242.6 link	c.-87+100T>C	intron_variant	Intron 1 of 7	2		ENSP00000362339.1	Q9NR31-1
SAR1A	ENST00000373239.2 link	c.-217+100T>C	intron_variant	Intron 1 of 4	3		ENSP00000362336.2	X1WI22

Frequencies

GnomAD3 genomes

AF:

0.000797

AC:

AN:

91642

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000438

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00229

Gnomad ASJ

AF:

0.00116

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.000400

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000650

Gnomad OTH

AF:

0.000829

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

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:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.000796

AC:

AN:

91668

Hom.:

Cov.:

AF XY:

0.000952

AC XY:

AN XY:

43086

show subpopulations

African (AFR)

AF:

0.000437

AC:

AN:

18320

American (AMR)

AF:

0.00229

AC:

AN:

9184

Ashkenazi Jewish (ASJ)

AF:

0.00116

AC:

AN:

2576

East Asian (EAS)

AF:

0.00

AC:

AN:

2690

South Asian (SAS)

AF:

0.00229

AC:

AN:

2620

European-Finnish (FIN)

AF:

0.000400

AC:

AN:

4994

Middle Eastern (MID)

AF:

0.00

AC:

AN:

202

European-Non Finnish (NFE)

AF:

0.000650

AC:

AN:

49256

Other (OTH)

AF:

0.000826

AC:

AN:

1210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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

-0.48

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

-0.17

PromoterAI

0.14

Neutral

(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