ENST00000430897.1:n.539+1873T>G

Variant names:

• chr2-11363225-A-C
• rs7424263
• ENST00000430897.1:n.539+1873T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430897.1(LINC03037):​n.539+1873T>G 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: LINC03037 ENST00000430897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 3 publications found

Genes affected

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

PPIAP60 (HGNC:53684): (peptidylprolyl isomerase A pseudogene 60)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PPIAP60	XM_047446546.1	c.502-1921A>C		intron_variant	Intron 2 of 3		XP_047302502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03037	ENST00000430897.1	n.539+1873T>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.311 AC: 12883 AN: 41394

American (AMR) AF: 0.180 AC: 2746 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3470

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5188

South Asian (SAS) AF: 0.0948 AC: 457 AN: 4822

European-Finnish (FIN) AF: 0.210 AC: 2217 AN: 10562

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14301 AN: 67968

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.209 Hom.: 5869

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7424263; hg19: chr2-11503351;