rs12032643

chr1-248874237-G-Achr1-248874237-G-Cchr1-248874237-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011544161.4(PGBD2):c.-48+345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,128 control chromosomes in the GnomAD database, including 1,846 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1846 hom., cov: 32)
• Consequence: PGBD2 XM_011544161.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.43

Genes affected

PGBD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGBD2	XM_011544161.4	c.-48+345G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21667 AN: 152010 Hom.: 1850 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.118

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21681 AN: 152128 Hom.: 1846 Cov.: 32 AF XY: 0.143 AC XY: 10669 AN XY: 74386

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.0758

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0925 Hom.: 422

Bravo AF: 0.142

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.0010
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12032643; hg19: chr1-249168436;