20-33083213-T-G

Variant names:

• chr20-33083213-T-G
• rs1453647973
• NM_182519.3:c.170-154T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_182519.3(BPIFB4):​c.170-154T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0023 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: BPIFB4 NM_182519.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 0 publications found

Genes affected

BPIFB4 (HGNC:16179): (BPI fold containing family B member 4) Predicted to enable lipid binding activity. Predicted to be located in cytoplasm and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFB4	NM_182519.3	c.170-154T>G		intron_variant	Intron 4 of 17	ENST00000375483.4	NP_872325.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFB4	ENST00000375483.4	c.170-154T>G		intron_variant	Intron 4 of 17	5	NM_182519.3	ENSP00000364632.3
BPIFB4	ENST00000674031.1	c.382T>G	p.Leu128Val	missense_variant	Exon 2 of 15			ENSP00000501266.1
BPIFB4	ENST00000445356.1	n.106+1581T>G		intron_variant	Intron 3 of 6	2		ENSP00000388423.1

Frequencies

GnomAD3 genomes AF: 0.00231 AC: 82 AN: 35558 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00320

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00329

Gnomad ASJ AF: 0.000926

Gnomad EAS AF: 0.00100

Gnomad SAS AF: 0.00602

Gnomad FIN AF: 0.00350

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.00429

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00233 AC: 83 AN: 35582 Hom.: 0 Cov.: 0 AF XY: 0.00269 AC XY: 44 AN XY: 16358

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00320 AC: 26 AN: 8128

American (AMR) AF: 0.00328 AC: 8 AN: 2436

Ashkenazi Jewish (ASJ) AF: 0.000926 AC: 1 AN: 1080

East Asian (EAS) AF: 0.00100 AC: 1 AN: 996

South Asian (SAS) AF: 0.00718 AC: 6 AN: 836

European-Finnish (FIN) AF: 0.00350 AC: 6 AN: 1714

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 34

European-Non Finnish (NFE) AF: 0.00169 AC: 33 AN: 19542

Other (OTH) AF: 0.00429 AC: 2 AN: 466

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.6
DANN	Benign	0.37
PhyloP100		-0.010
Mutation Taster		=100/0	polymorphism

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: rs1453647973; hg19: chr20-31671019;