20-33222046-C-T

Variant names:

• chr20-33222046-C-T
• rs1407015
• NM_178466.5:c.128-1765C>T

Variant summary

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

The NM_178466.5(BPIFA3):​c.128-1765C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,112 control chromosomes in the GnomAD database, including 3,502 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 0.12 (3502 hom., cov: 32)
• Consequence: BPIFA3 NM_178466.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFA3	NM_178466.5	c.128-1765C>T		intron_variant	Intron 1 of 6	ENST00000375454.8	NP_848561.2
BPIFA3	NM_001042439.2	c.128-1765C>T		intron_variant	Intron 1 of 5		NP_001035904.1
BPIFA3	XR_244132.4	n.355-1765C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFA3	ENST00000375454.8	c.128-1765C>T		intron_variant	Intron 1 of 6	5	NM_178466.5	ENSP00000364603.3
BPIFA3	ENST00000375452.3	c.128-1765C>T		intron_variant	Intron 1 of 5	1		ENSP00000364601.3
BPIFA3	ENST00000490499.5	n.355-1410C>T		intron_variant	Intron 1 of 6	1
BPIFA3	ENST00000471233.1	n.338-1765C>T		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17720 AN: 151994 Hom.: 3490 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00312

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00194

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.117 AC: 17782 AN: 152112 Hom.: 3502 Cov.: 32 AF XY: 0.114 AC XY: 8458 AN XY: 74358

African (AFR) AF: 0.405 AC: 16787 AN: 41454

American (AMR) AF: 0.0420 AC: 642 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00270 AC: 13 AN: 4806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00194 AC: 132 AN: 68018

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.0723 Hom.: 263

Bravo AF: 0.133

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		-1.1
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: rs1407015; hg19: chr20-31809852;