rs7424263

Variant names:

• chr2-11363225-A-C
• rs7424263
• XM_047446546.1:c.502-1921A>C

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

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

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430897.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03037	ENST00000430897.1	TSL:2	n.539+1873T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7424263;

hg19: chr2-11503351;