chr6-29507262-G-T

Variant names:

• chr6-29507262-G-T
• rs734961
• ENST00000436804.3:n.218G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183359.1(LINC02829):​n.216G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,362 control chromosomes in the GnomAD database, including 1,531 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 0.14 (1530 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: LINC02829 NR_183359.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 10 publications found

Genes affected

LINC02829 (HGNC:54362): (long intergenic non-protein coding RNA 2829)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183359.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02829	NR_183359.1		n.216G>T		non_coding_transcript_exon	Exon 3 of 4
	LINC02829	NR_183360.1		n.284G>T		non_coding_transcript_exon	Exon 4 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02829	ENST00000436804.3	TSL:5	n.218G>T		non_coding_transcript_exon	Exon 3 of 4
	LINC02829	ENST00000661850.2		n.347G>T		non_coding_transcript_exon	Exon 3 of 3
	LINC02829	ENST00000824900.1		n.286G>T		non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20756 AN: 152134 Hom.: 1525 Cov.: 33

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.118 AC: 13 AN: 110 Hom.: 1 Cov.: 0 AF XY: 0.125 AC XY: 11 AN XY: 88

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.146 AC: 12 AN: 82

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.136 AC: 20763 AN: 152252 Hom.: 1530 Cov.: 33 AF XY: 0.139 AC XY: 10336 AN XY: 74442

African (AFR) AF: 0.0758 AC: 3151 AN: 41556

American (AMR) AF: 0.181 AC: 2775 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1211 AN: 5170

South Asian (SAS) AF: 0.155 AC: 746 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1546 AN: 10600

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10366 AN: 68018

Other (OTH) AF: 0.141 AC: 298 AN: 2114

Alfa AF: 0.133 Hom.: 1348

Bravo AF: 0.141

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.28
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs734961; hg19: chr6-29475039;