2-11363225-A-C

Position:

• chr2-11363225-A-C

Variant summary

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

The XM_047446546.1(PPIAP60):​c.502-1921A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,994 control chromosomes in the GnomAD database, including 4,257 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 0.22 (4257 hom., cov: 32)
• Consequence: PPIAP60 XM_047446546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

PPIAP60 (HGNC:):

LINC03037 (HGNC:56227): (long intergenic non-protein coding RNA 3037)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPIAP60	XM_047446546.1	c.502-1921A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03037	ENST00000430897.1	n.539+1873T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34138 AN: 151876 Hom.: 4259 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.225 AC: 34156 AN: 151994 Hom.: 4257 Cov.: 32 AF XY: 0.221 AC XY: 16424 AN XY: 74292

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0948

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.200

Alfa AF: 0.205 Hom.: 4462

Bravo AF: 0.227

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7424263; hg19: chr2-11503351;