rs3131020

Variant names:

• chr6-29508125-C-T
• rs3131020
• ENST00000436804.3:n.624+457C>T

Variant summary

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

The ENST00000436804.3(LINC02829):​n.624+457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,962 control chromosomes in the GnomAD database, including 17,476 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 0.47 (17476 hom., cov: 32)
• Consequence: LINC02829 ENST00000436804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 23 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436804.3. 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.622+457C>T		intron	N/A
	LINC02829	NR_183360.1		n.690+457C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02829	ENST00000436804.3	TSL:5	n.624+457C>T		intron	N/A
	LINC02829	ENST00000824900.1		n.692+457C>T		intron	N/A
	LINC02829	ENST00000824901.1		n.757+457C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71743 AN: 151844 Hom.: 17444 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.473 AC: 71820 AN: 151962 Hom.: 17476 Cov.: 32 AF XY: 0.473 AC XY: 35164 AN XY: 74276

African (AFR) AF: 0.562 AC: 23282 AN: 41422

American (AMR) AF: 0.360 AC: 5500 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1974 AN: 5162

South Asian (SAS) AF: 0.601 AC: 2900 AN: 4822

European-Finnish (FIN) AF: 0.521 AC: 5507 AN: 10560

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30193 AN: 67946

Other (OTH) AF: 0.434 AC: 914 AN: 2108

Alfa AF: 0.453 Hom.: 45529

Bravo AF: 0.460

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.61
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs3131020; hg19: chr6-29475902;