NM_182519.3:c.169+107T>A

Variant names:

• chr20-33083107-T-A
• rs979395810
• NM_182519.3:c.169+107T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_182519.3(BPIFB4):​c.169+107T>A 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: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BPIFB4 NM_182519.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• 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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFB4	NM_182519.3	c.169+107T>A		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.169+107T>A		intron_variant	Intron 4 of 17	5	NM_182519.3	ENSP00000364632.3
BPIFB4	ENST00000674031.1	c.276T>A	p.Gly92Gly	synonymous_variant	Exon 2 of 15			ENSP00000501266.1
BPIFB4	ENST00000445356.1	n.106+1475T>A		intron_variant	Intron 3 of 6	2		ENSP00000388423.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 30202 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16476

African (AFR) AF: 0.00 AC: 0 AN: 492

American (AMR) AF: 0.00 AC: 0 AN: 1014

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 736

East Asian (EAS) AF: 0.00 AC: 0 AN: 838

South Asian (SAS) AF: 0.00 AC: 0 AN: 5548

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2584

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 106

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 17444

Other (OTH) AF: 0.00 AC: 0 AN: 1440

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	15
DANN	Benign	0.90
PhyloP100		0.18

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: rs979395810; hg19: chr20-31670913;