Variant 22-32445713-G-GAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BPIFC	NM_174932.3 linkuse as main transcript	c.531-17_531-16dupTT		intron_variant		ENST00000300399.9	NP_777592.1	Q8NFQ6-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
BPIFC	ENST00000300399.9 linkuse as main transcript	c.531-17_531-16dupTT	intron_variant	1	NM_174932.3	ENSP00000300399.3	Q8NFQ6-1
BPIFC	ENST00000397452.5 linkuse as main transcript	c.531-17_531-16dupTT	intron_variant	5		ENSP00000380594.1	Q8NFQ6-1
BPIFC	ENST00000534972.4 linkuse as main transcript	n.236-17_236-16dupTT	intron_variant	5		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

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.227

Gnomad4 EAS exome

AF:

0.185

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.187

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.259

AC:

19802

AN:

76332

Hom.:

2997

Cov.:

AF XY:

0.256

AC XY:

8588

AN XY:

33534

show subpopulations

Gnomad4 AFR

AF:

0.320

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.327

Gnomad4 EAS

AF:

0.259

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.230

Gnomad4 OTH

AF:

0.291

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 08, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over