22-32445713-GAAAAAAAAAAAA-GA

Variant names:

• chr22-32445713-GAAAAAAAAAAA-G
• rs61507713
• NM_174932.3:c.531-26_531-16delTTTTTTTTTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_174932.3(BPIFC):​c.531-26_531-16delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00663 in 711,352 control chromosomes in the GnomAD database, including 140 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.032 (98 hom., cov: 0)
  • Exomes 𝑓: 0.0036 (42 hom.)
• Consequence: BPIFC NM_174932.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 0 publications found

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]

BPIFC Gene-Disease associations (from GenCC):

• trichilemmal cyst

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174932.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPIFC	NM_174932.3	MANE Select	c.531-26_531-16delTTTTTTTTTTT		intron	N/A	NP_777592.1	Q8NFQ6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPIFC	ENST00000300399.9	TSL:1 MANE Select	c.531-26_531-16delTTTTTTTTTTT		intron	N/A	ENSP00000300399.3	Q8NFQ6-1
	BPIFC	ENST00000397452.5	TSL:5	c.531-26_531-16delTTTTTTTTTTT		intron	N/A	ENSP00000380594.1	Q8NFQ6-1
	BPIFC	ENST00000534972.4	TSL:5	n.*236-26_*236-16delTTTTTTTTTTT		intron	N/A	ENSP00000439123.3	A0A8C8NLL8

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 2449 AN: 76624 Hom.: 97 Cov.: 0

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0133

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00257

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000117

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.00356 AC: 2262 AN: 634712 Hom.: 42 AF XY: 0.00298 AC XY: 957 AN XY: 320834

African (AFR) AF: 0.118 AC: 1943 AN: 16416

American (AMR) AF: 0.00725 AC: 106 AN: 14630

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11646

East Asian (EAS) AF: 0.00 AC: 0 AN: 23836

South Asian (SAS) AF: 0.000204 AC: 8 AN: 39224

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22428

Middle Eastern (MID) AF: 0.00203 AC: 4 AN: 1966

European-Non Finnish (NFE) AF: 0.0000420 AC: 20 AN: 476524

Other (OTH) AF: 0.00645 AC: 181 AN: 28042

GnomAD4 genome AF: 0.0320 AC: 2456 AN: 76640 Hom.: 98 Cov.: 0 AF XY: 0.0338 AC XY: 1140 AN XY: 33690

African (AFR) AF: 0.114 AC: 2360 AN: 20706

American (AMR) AF: 0.0133 AC: 67 AN: 5030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2324

East Asian (EAS) AF: 0.00 AC: 0 AN: 2014

South Asian (SAS) AF: 0.00259 AC: 4 AN: 1544

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 694

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 76

European-Non Finnish (NFE) AF: 0.000117 AC: 5 AN: 42670

Other (OTH) AF: 0.0200 AC: 20 AN: 998

Alfa AF: 0.00 Hom.: 131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61507713; hg19: chr22-32841700;