rs17396317

chr20-33202571-G-Achr20-33202571-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026760.1(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 NR_026760.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPIFA4P	NR_026760.1	n.464G>A		non_coding_transcript_exon_variant	5/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFA4P	ENST00000375465.7	n.464G>A		non_coding_transcript_exon_variant	5/9	1
BPIFA4P	ENST00000420169.4	n.433G>A		non_coding_transcript_exon_variant	4/5	1
BPIFA4P	ENST00000603168.3	n.413G>A		non_coding_transcript_exon_variant	4/7

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10886 AN: 152084 Hom.: 554 Cov.: 32

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.: 7 Cov.: 0 AF XY: 0.0671 AC XY: 55 AN XY: 820

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.0723

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.0715 AC: 10887 AN: 152202 Hom.: 554 Cov.: 32 AF XY: 0.0689 AC XY: 5125 AN XY: 74404

Gnomad4 AFR AF: 0.0197

Gnomad4 AMR AF: 0.0432

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0701

Gnomad4 FIN AF: 0.0680

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0904 Hom.: 492

Bravo AF: 0.0681

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.014
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17396317; hg19: chr20-31790377;