dbSNP rs17092784: ERGIC3:c.686-528G>A (chr20-35554516-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_015966.3(ERGIC3):c.686-528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 950,496 control chromosomes in the GnomAD database, including 15,304 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 0.17 ( 2471 hom., cov: 31)

Exomes 𝑓: 0.18 ( 12833 hom. )

Consequence

ERGIC3
NM_015966.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.939

Publications

17 publications found

Variant links:

Genes affected

ERGIC3 (HGNC:15927): (ERGIC and golgi 3) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ERGIC3 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 (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015966.3. 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
	ERGIC3	NM_015966.3	MANE Select	c.686-528G>A		intron	N/A	NP_057050.1	A2TJK5
	ERGIC3	NM_198398.2		c.700+130G>A		intron	N/A	NP_938408.1	Q9Y282-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ERGIC3	ENST00000348547.7	TSL:1 MANE Select	c.686-528G>A	intron	N/A	ENSP00000341358.2	Q9Y282-1
ERGIC3	ENST00000955795.1		c.686-528G>A	intron	N/A	ENSP00000625854.1
ERGIC3	ENST00000955798.1		c.745+130G>A	intron	N/A	ENSP00000625857.1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26380

AN:

152030

Hom.:

2471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.195

GnomAD4 exome

AF:

0.176

AC:

140143

AN:

798348

Hom.:

12833

AF XY:

0.181

AC XY:

75005

AN XY:

415324

show subpopulations

African (AFR)

AF:

0.190

AC:

3818

AN:

20086

American (AMR)

AF:

0.195

AC:

6485

AN:

33218

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

4591

AN:

18024

East Asian (EAS)

AF:

0.125

AC:

4564

AN:

36532

South Asian (SAS)

AF:

0.288

AC:

18162

AN:

63138

European-Finnish (FIN)

AF:

0.110

AC:

5408

AN:

49006

Middle Eastern (MID)

AF:

0.281

AC:

807

AN:

2876

European-Non Finnish (NFE)

AF:

0.166

AC:

89331

AN:

537290

Other (OTH)

AF:

0.183

AC:

6977

AN:

38178

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

5728

11456

17184

22912

28640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2218

4436

6654

8872

11090

<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:

0.173

AC:

26389

AN:

152148

Hom.:

2471

Cov.:

AF XY:

0.173

AC XY:

12862

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.180

AC:

7482

AN:

41478

American (AMR)

AF:

0.206

AC:

3143

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

879

AN:

3468

East Asian (EAS)

AF:

0.143

AC:

742

AN:

5178

South Asian (SAS)

AF:

0.292

AC:

1409

AN:

4826

European-Finnish (FIN)

AF:

0.111

AC:

1172

AN:

10596

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10949

AN:

68010

Other (OTH)

AF:

0.195

AC:

411

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1109

2218

3328

4437

5546

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.155

Hom.:

1056

Bravo

AF:

0.177

Asia WGS

AF:

0.231

AC:

804

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.9

(source)

DANN

Benign

0.52

PhyloP100

0.94

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over