20-33210631-T-C

Variant names:

• chr20-33210631-T-C
• rs17124372
• ENST00000375465.7:n.*169T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

Genes affected

BPIFA4P (HGNC:):

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=-0.81).
• 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	n.*169T>C		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9148 AN: 152110 Hom.: 461 Cov.: 32

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.: 32 AF XY: 0.0581 AC XY: 4325 AN XY: 74448

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0328

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0307 Hom.: 106

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
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17124372; hg19: chr20-31798437;