Genetic Variant BPIFA4P:n.*169T>C (chr20-33210631-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000375465.7(BPIFA4P):n.*169T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,230 control chromosomes in the GnomAD database, including 458 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 0.060 ( 458 hom., cov: 32)

Consequence

BPIFA4P
ENST00000375465.7 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.815

Publications

4 publications found

Variant links:

Genes affected

BPIFA4P (HGNC:):

BPIFA4P links:

BPIFA4P (HGNC:20469): (BPI fold containing family A member 4, pseudogene) Predicted to enable lipid binding activity. Predicted to be involved in regulation of liquid surface tension. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

BPIFA4P 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFA4P	NR_026760.1 link	n.*169T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFA4P	ENST00000375465.7 link	n.*169T>C		downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0601

AC:

9148

AN:

152110

Hom.:

461

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0308

Gnomad AMR

AF:

0.0311

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.0189

Gnomad SAS

AF:

0.0137

Gnomad FIN

AF:

0.0399

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0328

Gnomad OTH

AF:

0.0468

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0601

AC:

9156

AN:

152230

Hom.:

458

Cov.:

AF XY:

0.0581

AC XY:

4325

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.137

AC:

5670

AN:

41504

American (AMR)

AF:

0.0310

AC:

474

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3472

East Asian (EAS)

AF:

0.0187

AC:

AN:

5184

South Asian (SAS)

AF:

0.0137

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0399

AC:

424

AN:

10618

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0328

AC:

2229

AN:

68014

Other (OTH)

AF:

0.0482

AC:

102

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

420

839

1259

1678

2098

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0368

Hom.:

418

Bravo

AF:

0.0627

Asia WGS

AF:

0.0400

AC:

137

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.3

(source)

DANN

Benign

0.73

PhyloP100

-0.81

Splicing

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

Publications

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20-33210631-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over