rs10822036

Variant names:

• chr10-62614600-G-A
• rs10822036
• ENST00000647733.1:c.982-8503G>A

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.982-8503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,098 control chromosomes in the GnomAD database, including 3,037 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 0.20 (3037 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

Genes affected

ENSG00000285837 (HGNC:):

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 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
ENSG00000285837	ENST00000647733.1	c.982-8503G>A		intron_variant	Intron 4 of 7			ENSP00000502188.1
LINC02929	ENST00000395251.5	n.151-29142G>A		intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29950 AN: 151980 Hom.: 3034 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.197 AC: 29982 AN: 152098 Hom.: 3037 Cov.: 32 AF XY: 0.202 AC XY: 15039 AN XY: 74370

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.193

Alfa AF: 0.179 Hom.: 3161

Bravo AF: 0.192

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.55
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10822036; hg19: chr10-64374360;