ENST00000562660.1:n.86+813C>T

Variant names:

• chr15-62269782-G-A
• rs2037276
• ENST00000562660.1:n.86+813C>T

Variant summary

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

The ENST00000562660.1(GOLGA2P11):​n.86+813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,088 control chromosomes in the GnomAD database, including 6,777 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 0.29 (6777 hom., cov: 32)
• Consequence: GOLGA2P11 ENST00000562660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

GOLGA2P11 (HGNC:26788): (GOLGA2 pseudogene 11)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA2P11	ENST00000562660.1	n.86+813C>T		intron_variant	Intron 1 of 17	6

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44382 AN: 151972 Hom.: 6755 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.292 AC: 44440 AN: 152088 Hom.: 6777 Cov.: 32 AF XY: 0.292 AC XY: 21733 AN XY: 74354

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.276

Alfa AF: 0.259 Hom.: 2769

Bravo AF: 0.304

Asia WGS AF: 0.365 AC: 1270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037276; hg19: chr15-62561981;