chr20-33218782-T-C

Variant names:

• chr20-33218782-T-C
• rs17305657
• NM_178466.5:c.127+1119T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178466.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPIFA3	NM_178466.5	MANE Select	c.127+1119T>C		intron	N/A	NP_848561.2
	BPIFA3	NM_001042439.2		c.127+1119T>C		intron	N/A	NP_001035904.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPIFA3	ENST00000375454.8	TSL:5 MANE Select	c.127+1119T>C		intron	N/A	ENSP00000364603.3
	BPIFA3	ENST00000375452.3	TSL:1	c.127+1119T>C		intron	N/A	ENSP00000364601.3
	BPIFA3	ENST00000490499.5	TSL:1	n.354+1119T>C		intron	N/A

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

African (AFR) AF: 0.0141 AC: 586 AN: 41542

American (AMR) AF: 0.0354 AC: 541 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.00767 AC: 37 AN: 4824

European-Finnish (FIN) AF: 0.0470 AC: 498 AN: 10586

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0849 AC: 5774 AN: 68004

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0710 Hom.: 947

Bravo AF: 0.0503

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.42
PhyloP100		0.0010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17305657; hg19: chr20-31806588;