22-32445713-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_174932.3(BPIFC):c.531-16_531-15insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 699,088 control chromosomes in the GnomAD database, including 4,628 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.27 (3041 hom., cov: 0)
  • Exomes 𝑓: 0.21 (1587 hom.)
• Consequence: BPIFC NM_174932.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0980

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 -10 ACMG points.

• BP6: Variant 22-32445713-G-GA is Benign according to our data. Variant chr22-32445713-G-GA is described in ClinVar as [Benign]. Clinvar id is 2798125.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPIFC	NM_174932.3	c.531-16_531-15insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000300399.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFC	ENST00000300399.9	c.531-16_531-15insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_174932.3	P1
BPIFC	ENST00000397452.5	c.531-16_531-15insT		splice_polypyrimidine_tract_variant, intron_variant		5		P1
BPIFC	ENST00000534972.4	c.*236-16_*236-15insT		splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.269 AC: 20532 AN: 76370 Hom.: 3040 Cov.: 0

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.280

GnomAD4 exome AF: 0.209 AC: 130280 AN: 622706 Hom.: 1587 Cov.: 25 AF XY: 0.206 AC XY: 64657 AN XY: 314582

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.206

Gnomad4 EAS exome AF: 0.185

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.221

Gnomad4 OTH exome AF: 0.204

GnomAD4 genome AF: 0.269 AC: 20533 AN: 76382 Hom.: 3041 Cov.: 0 AF XY: 0.264 AC XY: 8877 AN XY: 33594

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.280

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 29, 2023

- -

Computational scores

Source: dbNSFP v4.3

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: rs61507713; hg19: chr22-32841700;