rs17305657

chr20-33218782-T-C

Variant summary

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

The NM_178466.5(BPIFA3):c.127+1119T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 152,214 control chromosomes in the GnomAD database, including 307 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 0.051 (307 hom., cov: 32)
• Consequence: BPIFA3 NM_178466.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

BPIFA3 (HGNC:16204): (BPI fold containing family A member 3) Predicted to enable lipid binding activity. 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPIFA3	NM_178466.5	c.127+1119T>C		intron_variant		ENST00000375454.8
BPIFA3	NM_001042439.2	c.127+1119T>C		intron_variant
BPIFA3	XR_244132.4	n.354+1119T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFA3	ENST00000375454.8	c.127+1119T>C		intron_variant		5	NM_178466.5	P1
BPIFA3	ENST00000375452.3	c.127+1119T>C		intron_variant		1
BPIFA3	ENST00000490499.5	n.354+1119T>C		intron_variant, non_coding_transcript_variant		1
BPIFA3	ENST00000471233.1	n.337+1119T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7783 AN: 152098 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0511 AC: 7784 AN: 152214 Hom.: 307 Cov.: 32 AF XY: 0.0477 AC XY: 3550 AN XY: 74444

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00767

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0711 Hom.: 684

Bravo AF: 0.0503

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.25
Dann	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17305657; hg19: chr20-31806588;