dbSNP rs17396317: BPIFA4P:n.464G>A (chr20-33202571-G-A) – 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.464G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 153,780 control chromosomes in the GnomAD database, including 561 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 0.072 ( 554 hom., cov: 32)

Exomes 𝑓: 0.074 ( 7 hom. )

Consequence

BPIFA4P
ENST00000375465.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.52

Publications

10 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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new If you want to explore the variant's impact on the transcript ENST00000375465.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375465.7. 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
	BPIFA4P	NR_026760.1		n.464G>A		non_coding_transcript_exon	Exon 5 of 9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
BPIFA4P	ENST00000375465.7	TSL:1	n.464G>A	non_coding_transcript_exon	Exon 5 of 9
BPIFA4P	ENST00000420169.4	TSL:1	n.433G>A	non_coding_transcript_exon	Exon 4 of 5
BPIFA4P	ENST00000603168.3	TSL:6	n.413G>A	non_coding_transcript_exon	Exon 4 of 7

Frequencies

GnomAD3 genomes

AF:

0.0716

AC:

10886

AN:

152084

Hom.:

554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0197

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.0433

Gnomad ASJ

AF:

0.0640

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0701

Gnomad FIN

AF:

0.0680

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.0512

GnomAD4 exome

AF:

0.0735

AC:

116

AN:

1578

Hom.:

Cov.:

AF XY:

0.0671

AC XY:

AN XY:

820

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0723

AC:

111

AN:

1536

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.150

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0715

AC:

10887

AN:

152202

Hom.:

554

Cov.:

AF XY:

0.0689

AC XY:

5125

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0197

AC:

817

AN:

41562

American (AMR)

AF:

0.0432

AC:

661

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0640

AC:

222

AN:

3468

East Asian (EAS)

AF:

0.00135

AC:

AN:

5176

South Asian (SAS)

AF:

0.0701

AC:

337

AN:

4806

European-Finnish (FIN)

AF:

0.0680

AC:

720

AN:

10588

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7832

AN:

67988

Other (OTH)

AF:

0.0507

AC:

107

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

497

994

1491

1988

2485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0817

Hom.:

824

Bravo

AF:

0.0681

Asia WGS

AF:

0.0320

AC:

110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.014

(source)

DANN

Benign

0.56

PhyloP100

-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over