22-32445713-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant names:

• chr22-32445713-G-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
• rs61507713
• NM_174932.3:c.531-16_531-15insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

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

The NM_174932.3(BPIFC):​c.531-16_531-15insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000788 in 634,728 control chromosomes in the GnomAD database, including 2 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type INS_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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000079 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: BPIFC NM_174932.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• 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 GnomAdExome4 at 5 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.531-16_531-15insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT		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.531-16_531-15insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000300399.3	Q8NFQ6-1
	BPIFC	ENST00000397452.5	TSL:5	c.531-16_531-15insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000380594.1	Q8NFQ6-1
	BPIFC	ENST00000534972.4	TSL:5	n.*236-16_*236-15insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000439123.3	A0A8C8NLL8

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 76586 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000788 AC: 5 AN: 634728 Hom.: 2 Cov.: 25 AF XY: 0.00000623 AC XY: 2 AN XY: 320842

African (AFR) AF: 0.00 AC: 0 AN: 16416

American (AMR) AF: 0.00 AC: 0 AN: 14630

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

East Asian (EAS) AF: 0.0000420 AC: 1 AN: 23836

South Asian (SAS) AF: 0.00 AC: 0 AN: 39224

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

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

European-Non Finnish (NFE) AF: 0.00000839 AC: 4 AN: 476538

Other (OTH) AF: 0.00 AC: 0 AN: 28044

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 76586 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 33648

African (AFR) AF: 0.00 AC: 0 AN: 20646

American (AMR) AF: 0.00 AC: 0 AN: 5022

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 2018

South Asian (SAS) AF: 0.00 AC: 0 AN: 1554

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: 0.00 AC: 0 AN: 42672

Other (OTH) AF: 0.00 AC: 0 AN: 996

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.098

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;