Genetic Variant BPIFC:c.531-17_531-16dupTT (chr22-32445713-G-GAA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_174932.3(BPIFC):c.531-17_531-16dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 691,780 control chromosomes in the GnomAD database, including 5,499 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 2997 hom., cov: 0)

Exomes 𝑓: 0.19 ( 2502 hom. )

Consequence

BPIFC
NM_174932.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0980

Publications

0 publications found

Variant links:

Genes affected

BPIFC (HGNC:16503): (BPI fold containing family C) Predicted to enable lipid binding activity. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

BPIFC Gene-Disease associations (from GenCC):

trichilemmal cyst
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

BPIFC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 22-32445713-G-GAA is Benign according to our data. Variant chr22-32445713-G-GAA is described in ClinVar as Benign. ClinVar VariationId is 2776152.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174932.3. 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
	BPIFC	NM_174932.3	MANE Select	c.531-17_531-16dupTT		intron	N/A	NP_777592.1	Q8NFQ6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BPIFC	ENST00000300399.9	TSL:1 MANE Select	c.531-16_531-15insTT	intron	N/A	ENSP00000300399.3	Q8NFQ6-1
BPIFC	ENST00000397452.5	TSL:5	c.531-16_531-15insTT	intron	N/A	ENSP00000380594.1	Q8NFQ6-1
BPIFC	ENST00000534972.4	TSL:5	n.236-16_236-15insTT	intron	N/A	ENSP00000439123.3	A0A8C8NLL8

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

19801

AN:

76310

Hom.:

2996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.327

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.395

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.186

AC:

114468

AN:

615448

Hom.:

2502

Cov.:

AF XY:

0.184

AC XY:

57269

AN XY:

310790

show subpopulations

African (AFR)

AF:

0.194

AC:

2983

AN:

15370

American (AMR)

AF:

0.188

AC:

2626

AN:

13946

Ashkenazi Jewish (ASJ)

AF:

0.227

AC:

2544

AN:

11198

East Asian (EAS)

AF:

0.185

AC:

4188

AN:

22634

South Asian (SAS)

AF:

0.163

AC:

6177

AN:

37866

European-Finnish (FIN)

AF:

0.169

AC:

3646

AN:

21538

Middle Eastern (MID)

AF:

0.208

AC:

395

AN:

1896

European-Non Finnish (NFE)

AF:

0.187

AC:

86632

AN:

463940

Other (OTH)

AF:

0.195

AC:

5277

AN:

27060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

4846

9693

14539

19386

24232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2890

5780

8670

11560

14450

<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:

0.259

AC:

19802

AN:

76332

Hom.:

2997

Cov.:

AF XY:

0.256

AC XY:

8588

AN XY:

33534

show subpopulations

African (AFR)

AF:

0.320

AC:

6528

AN:

20426

American (AMR)

AF:

0.268

AC:

1348

AN:

5036

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

764

AN:

2336

East Asian (EAS)

AF:

0.259

AC:

520

AN:

2010

South Asian (SAS)

AF:

0.177

AC:

273

AN:

1544

European-Finnish (FIN)

AF:

0.147

AC:

102

AN:

692

Middle Eastern (MID)

AF:

0.392

AC:

AN:

European-Non Finnish (NFE)

AF:

0.230

AC:

9805

AN:

42636

Other (OTH)

AF:

0.291

AC:

289

AN:

994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

550

1100

1649

2199

2749

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.103

Hom.:

131

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.098

Mutation Taster

=100/0

polymorphism

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over