rs2076054

chr22-32436887-C-T

Variant summary

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

The NM_174932.3(BPIFC):c.747+873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,118 control chromosomes in the GnomAD database, including 34,769 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 0.66 (34769 hom., cov: 33)
• Consequence: BPIFC NM_174932.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

Genes affected

BPIFC (HGNC:16503): (BPI fold containing family C) Predicted to enable lipid binding activity. Predicted to be active in extracellular space. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPIFC	NM_174932.3	c.747+873G>A		intron_variant		ENST00000300399.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFC	ENST00000300399.9	c.747+873G>A		intron_variant		1	NM_174932.3	P1
BPIFC	ENST00000397452.5	c.747+873G>A		intron_variant		5		P1
BPIFC	ENST00000534972.4	c.*452+873G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100488 AN: 152000 Hom.: 34746 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.661 AC: 100548 AN: 152118 Hom.: 34769 Cov.: 33 AF XY: 0.665 AC XY: 49399 AN XY: 74336

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.693

Alfa AF: 0.746 Hom.: 86185

Bravo AF: 0.649

Asia WGS AF: 0.759 AC: 2633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.27
Dann	Benign	0.58

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: rs2076054; hg19: chr22-32832874;