22-32445713-G-GAAA

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_531-15insTTT 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 0.116 in 615,060 control chromosomes in the GnomAD database, including 2,161 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (1466 hom., cov: 0)
  • Exomes 𝑓: 0.12 (2161 hom.)
  • Failed GnomAD Quality Control
• 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-GAAA is Benign according to our data. Variant chr22-32445713-G-GAAA is described in ClinVar as [Benign]. Clinvar id is 2975955.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 12913 AN: 76340 Hom.: 1465 Cov.: 0

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.116 AC: 71410 AN: 615060 Hom.: 2161 Cov.: 25 AF XY: 0.117 AC XY: 36382 AN XY: 311036

Gnomad4 AFR exome AF: 0.0853

Gnomad4 AMR exome AF: 0.133

Gnomad4 ASJ exome AF: 0.129

Gnomad4 EAS exome AF: 0.121

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.112

Gnomad4 OTH exome AF: 0.122

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.169 AC: 12918 AN: 76356 Hom.: 1466 Cov.: 0 AF XY: 0.170 AC XY: 5705 AN XY: 33564

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.169

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

Jan 08, 2024

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Computational scores

Source: dbNSFP v4.3

Splicing

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;