22-32445713-GAAAAAAAAAAAA-GAAAAAAA

Variant names:

• chr22-32445713-GAAAAA-G
• rs61507713
• NM_174932.3:c.531-20_531-16delTTTTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_174932.3(BPIFC):​c.531-20_531-16delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000266 in 711,208 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00031 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00026 (1 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 24 AD gene.

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.531-20_531-16delTTTTT		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.531-20_531-16delTTTTT		intron	N/A	ENSP00000300399.3	Q8NFQ6-1
	BPIFC	ENST00000397452.5	TSL:5	c.531-20_531-16delTTTTT		intron	N/A	ENSP00000380594.1	Q8NFQ6-1
	BPIFC	ENST00000534972.4	TSL:5	n.*236-20_*236-16delTTTTT		intron	N/A	ENSP00000439123.3	A0A8C8NLL8

Frequencies

GnomAD3 genomes AF: 0.000313 AC: 24 AN: 76586 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0000484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00199

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000496

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000258

Gnomad OTH AF: 0.00100

GnomAD4 exome AF: 0.000260 AC: 165 AN: 634608 Hom.: 1 AF XY: 0.000287 AC XY: 92 AN XY: 320766

African (AFR) AF: 0.000305 AC: 5 AN: 16414

American (AMR) AF: 0.00185 AC: 27 AN: 14622

Ashkenazi Jewish (ASJ) AF: 0.000258 AC: 3 AN: 11646

East Asian (EAS) AF: 0.000252 AC: 6 AN: 23828

South Asian (SAS) AF: 0.000128 AC: 5 AN: 39212

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22426

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1966

European-Non Finnish (NFE) AF: 0.000233 AC: 111 AN: 476460

Other (OTH) AF: 0.000285 AC: 8 AN: 28034

GnomAD4 genome AF: 0.000313 AC: 24 AN: 76600 Hom.: 1 Cov.: 0 AF XY: 0.000386 AC XY: 13 AN XY: 33664

African (AFR) AF: 0.0000484 AC: 1 AN: 20668

American (AMR) AF: 0.00199 AC: 10 AN: 5028

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

East Asian (EAS) AF: 0.000497 AC: 1 AN: 2014

South Asian (SAS) AF: 0.00 AC: 0 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: 0.000258 AC: 11 AN: 42670

Other (OTH) AF: 0.00100 AC: 1 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;