Genetic Variant BPIFC:c.531-22_531-16delTTTTTTT (chr22-32445713-GAAAAAAA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_174932.3(BPIFC):c.531-22_531-16delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 711,308 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0050 ( 5 hom., cov: 0)

Exomes 𝑓: 0.00072 ( 0 hom. )

Consequence

BPIFC
NM_174932.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.416

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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.005 (383/76598) while in subpopulation AFR AF = 0.0177 (365/20666). AF 95% confidence interval is 0.0162. There are 5 homozygotes in GnomAd4. There are 185 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High AC in GnomAd4 at 383 AD gene.

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.531-22_531-16delTTTTTTT		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.531-22_531-16delTTTTTTT	intron	N/A	ENSP00000300399.3	Q8NFQ6-1
BPIFC	ENST00000397452.5	TSL:5	c.531-22_531-16delTTTTTTT	intron	N/A	ENSP00000380594.1	Q8NFQ6-1
BPIFC	ENST00000534972.4	TSL:5	n.236-22_236-16delTTTTTTT	intron	N/A	ENSP00000439123.3	A0A8C8NLL8

Frequencies

GnomAD3 genomes

AF:

0.00497

AC:

381

AN:

76584

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0176

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00239

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000937

Gnomad OTH

AF:

0.00201

GnomAD4 exome

AF:

0.000717

AC:

455

AN:

634710

Hom.:

AF XY:

0.000676

AC XY:

217

AN XY:

320828

show subpopulations

African (AFR)

AF:

0.0185

AC:

304

AN:

16408

American (AMR)

AF:

0.00403

AC:

AN:

14630

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11646

East Asian (EAS)

AF:

0.00

AC:

AN:

23836

South Asian (SAS)

AF:

0.000229

AC:

AN:

39224

European-Finnish (FIN)

AF:

0.00

AC:

AN:

22428

Middle Eastern (MID)

AF:

0.00102

AC:

AN:

1966

European-Non Finnish (NFE)

AF:

0.0000776

AC:

AN:

476528

Other (OTH)

AF:

0.00157

AC:

AN:

28044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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:

0.00500

AC:

383

AN:

76598

Hom.:

Cov.:

AF XY:

0.00550

AC XY:

185

AN XY:

33664

show subpopulations

African (AFR)

AF:

0.0177

AC:

365

AN:

20666

American (AMR)

AF:

0.00239

AC:

AN:

5028

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2324

East Asian (EAS)

AF:

0.00

AC:

AN:

2014

South Asian (SAS)

AF:

0.00

AC:

AN:

1544

European-Finnish (FIN)

AF:

0.00

AC:

AN:

694

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000937

AC:

AN:

42670

Other (OTH)

AF:

0.00200

AC:

AN:

998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.586

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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.:

131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.42

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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22-32445713-GAAAAAAAAAAAA-GAAAAA

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