ENST00000647733.1:c.982-8503G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000285837 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647733.1. 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
	ENSG00000285837	ENST00000647733.1		c.982-8503G>A		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000395251.5	TSL:1	n.151-29142G>A		intron	N/A

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

African (AFR) AF: 0.206 AC: 8562 AN: 41476

American (AMR) AF: 0.203 AC: 3104 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1206 AN: 5162

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2580 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12213 AN: 67980

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.182 Hom.: 7971

Bravo AF: 0.192

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.55
DANN	Benign	0.65
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10822036; hg19: chr10-64374360;