rs2829459

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Variant has high frequency in the AFR (0.0221) population. However there is too low homozygotes in high coverage region: (expected more than 5, got 0).
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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
LINC01692	ENST00000762004.1	n.285+62132G>A		intron_variant	Intron 2 of 3

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0233 AC: 888 AN: 38040

American (AMR) AF: 0.0113 AC: 163 AN: 14484

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 43 AN: 3300

East Asian (EAS) AF: 0.00595 AC: 30 AN: 5038

South Asian (SAS) AF: 0.0142 AC: 65 AN: 4592

European-Finnish (FIN) AF: 0.00238 AC: 25 AN: 10510

Middle Eastern (MID) AF: 0.0106 AC: 3 AN: 282

European-Non Finnish (NFE) AF: 0.00701 AC: 464 AN: 66162

Other (OTH) AF: 0.0134 AC: 27 AN: 2014

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2829459; hg19: chr21-26279351;