rs17396317

Variant names:

• chr20-33202571-G-A
• rs17396317
• ENST00000375465.7:n.464G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-33202571-G-A
• chr20-33202571-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 10 publications found

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFA4P	NR_026760.1	n.464G>A		non_coding_transcript_exon_variant	Exon 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFA4P	ENST00000375465.7	n.464G>A		non_coding_transcript_exon_variant	Exon 5 of 9	1
BPIFA4P	ENST00000420169.4	n.433G>A		non_coding_transcript_exon_variant	Exon 4 of 5	1
BPIFA4P	ENST00000603168.3	n.413G>A		non_coding_transcript_exon_variant	Exon 4 of 7	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0723 AC: 111 AN: 1536

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.150 AC: 3 AN: 20

Other (OTH) AF: 0.100 AC: 2 AN: 20

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

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: 7 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: 9 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7832 AN: 67988

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.014
DANN	Benign	0.56
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs17396317; hg19: chr20-31790377;