Genetic Variant NM_006217.6:c.*63G>A (chr3-167442046-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006217.6(SERPINI2):c.*63G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,272,632 control chromosomes in the GnomAD database, including 13,486 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 0.19 ( 4133 hom., cov: 33)

Exomes 𝑓: 0.11 ( 9353 hom. )

Consequence

SERPINI2
NM_006217.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318

Publications

13 publications found

Variant links:

Genes affected

SERPINI2 (HGNC:8945): (serpin family I member 2) The gene encodes a member of a family of proteins that acts as inhibitors of serine proteases. These proteins function in the regulation of a variety of physiological processes, including coagulation, fibrinolysis, development, malignancy, and inflammation. Expression of the encoded protein may be downregulated during pancreatic carcinogenesis. Alternative splicing results in multiple transcript variants for this gene. [provided by RefSeq, Jan 2013]

SERPINI2 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006217.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SERPINI2	NM_006217.6	MANE Select	c.*63G>A	3_prime_UTR	Exon 9 of 9	NP_006208.1
SERPINI2	NM_001012303.3		c.*63G>A	3_prime_UTR	Exon 10 of 10	NP_001012303.2
SERPINI2	NM_001394327.1		c.*63G>A	3_prime_UTR	Exon 10 of 10	NP_001381256.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SERPINI2	ENST00000264677.9	TSL:1 MANE Select	c.*63G>A	3_prime_UTR	Exon 9 of 9	ENSP00000264677.4
SERPINI2	ENST00000461846.5	TSL:1	c.*63G>A	3_prime_UTR	Exon 9 of 9	ENSP00000417692.1
SERPINI2	ENST00000471111.5	TSL:1	c.*63G>A	downstream_gene	N/A	ENSP00000419407.1

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29064

AN:

151788

Hom.:

4117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.398

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.0925

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.0897

Gnomad OTH

AF:

0.155

GnomAD4 exome

AF:

0.107

AC:

120068

AN:

1120726

Hom.:

9353

Cov.:

AF XY:

0.105

AC XY:

59766

AN XY:

567340

show subpopulations

African (AFR)

AF:

0.401

AC:

9755

AN:

24298

American (AMR)

AF:

0.245

AC:

7472

AN:

30546

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

2573

AN:

21754

East Asian (EAS)

AF:

0.326

AC:

11784

AN:

36134

South Asian (SAS)

AF:

0.0808

AC:

5539

AN:

68556

European-Finnish (FIN)

AF:

0.103

AC:

4922

AN:

47760

Middle Eastern (MID)

AF:

0.122

AC:

609

AN:

4976

European-Non Finnish (NFE)

AF:

0.0850

AC:

71307

AN:

838552

Other (OTH)

AF:

0.127

AC:

6107

AN:

48150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

4680

9360

14039

18719

23399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2626

5252

7878

10504

13130

<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:

0.192

AC:

29129

AN:

151906

Hom.:

4133

Cov.:

AF XY:

0.189

AC XY:

14040

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.398

AC:

16448

AN:

41364

American (AMR)

AF:

0.173

AC:

2646

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

397

AN:

3470

East Asian (EAS)

AF:

0.291

AC:

1498

AN:

5144

South Asian (SAS)

AF:

0.0919

AC:

443

AN:

4820

European-Finnish (FIN)

AF:

0.100

AC:

1061

AN:

10568

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0897

AC:

6099

AN:

67960

Other (OTH)

AF:

0.160

AC:

337

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

1030

2060

3091

4121

5151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.108

Hom.:

1438

Bravo

AF:

0.212

Asia WGS

AF:

0.209

AC:

724

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.9

(source)

DANN

Benign

0.56

PhyloP100

0.32

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