rs2829459

Variant names:

• chr21-24907037-G-A
• rs2829459
• ENST00000441009.1:n.330+62108G>A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2 BP4_Strong BS1

The ENST00000441009.1(LINC01692):​n.330+62108G>A variant causes a intron change. The variant allele was found at a frequency of 0.0118 in 145,296 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.012 (0 hom., cov: 31)
• Consequence: LINC01692 ENST00000441009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

LINC01692 (HGNC:52480): (long intergenic non-protein coding RNA 1692)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0118 (1717/145296) while in subpopulation AFR AF= 0.0233 (888/38040). AF 95% confidence interval is 0.0221. There are 0 homozygotes in gnomad4. There are 862 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01692	NR_046198.3	n.330+62108G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01692	ENST00000441009.1	n.330+62108G>A		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.0118 AC: 1718 AN: 145184 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0103

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00633

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.00238

Gnomad MID AF: 0.0133

Gnomad NFE AF: 0.00703

Gnomad OTH AF: 0.0136

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

GnomAD4 genome AF: 0.0118 AC: 1717 AN: 145296 Hom.: 0 Cov.: 31 AF XY: 0.0121 AC XY: 862 AN XY: 71188

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0113

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00595

Gnomad4 SAS AF: 0.0142

Gnomad4 FIN AF: 0.00238

Gnomad4 NFE AF: 0.00701

Gnomad4 OTH AF: 0.0134

Alfa AF: 0.0194 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2829459; hg19: chr21-26279351;