Genetic Variant NM_174932.3:c.531-16dupT (chr22-32445713-G-GA) – 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.531-16dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 699,088 control chromosomes in the GnomAD database, including 4,628 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 3041 hom., cov: 0)

Exomes 𝑓: 0.21 ( 1587 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-GA is Benign according to our data. Variant chr22-32445713-G-GA is described in ClinVar as Benign. ClinVar VariationId is 2798125.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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.531-16dupT		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_531-15insT	intron	N/A	ENSP00000300399.3	Q8NFQ6-1
BPIFC	ENST00000397452.5	TSL:5	c.531-16_531-15insT	intron	N/A	ENSP00000380594.1	Q8NFQ6-1
BPIFC	ENST00000534972.4	TSL:5	n.236-16_236-15insT	intron	N/A	ENSP00000439123.3	A0A8C8NLL8

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

20532

AN:

76370

Hom.:

3040

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.303

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.280

GnomAD4 exome

AF:

0.209

AC:

130280

AN:

622706

Hom.:

1587

Cov.:

AF XY:

0.206

AC XY:

64657

AN XY:

314582

show subpopulations

African (AFR)

AF:

0.167

AC:

2612

AN:

15682

American (AMR)

AF:

0.149

AC:

2105

AN:

14162

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

2347

AN:

11388

East Asian (EAS)

AF:

0.185

AC:

4292

AN:

23148

South Asian (SAS)

AF:

0.128

AC:

4892

AN:

38160

European-Finnish (FIN)

AF:

0.190

AC:

4166

AN:

21908

Middle Eastern (MID)

AF:

0.219

AC:

425

AN:

1940

European-Non Finnish (NFE)

AF:

0.221

AC:

103841

AN:

468892

Other (OTH)

AF:

0.204

AC:

5600

AN:

27426

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.401

Heterozygous variant carriers

5222

10444

15666

20888

26110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3576

7152

10728

14304

17880

<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:

0.269

AC:

20533

AN:

76382

Hom.:

3041

Cov.:

AF XY:

0.264

AC XY:

8877

AN XY:

33594

show subpopulations

African (AFR)

AF:

0.231

AC:

4737

AN:

20510

American (AMR)

AF:

0.224

AC:

1124

AN:

5018

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

606

AN:

2330

East Asian (EAS)

AF:

0.152

AC:

306

AN:

2008

South Asian (SAS)

AF:

0.224

AC:

344

AN:

1536

European-Finnish (FIN)

AF:

0.208

AC:

145

AN:

696

Middle Eastern (MID)

AF:

0.224

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

12798

AN:

42626

Other (OTH)

AF:

0.280

AC:

279

AN:

998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

533

1066

1599

2132

2665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.130

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

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