rs10822036

Positions:

• chr10-62614600-G-A

Variant summary

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

The ENST00000395251.5(LINC02929):​n.151-29142G>A variant causes a intron, non coding transcript 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: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

Genes affected

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.151-29142G>A		intron_variant, non_coding_transcript_variant		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;