rs2829459

Positions:

• chr21-24907037-G-A

Variant summary

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

The NR_046198.3(LINC01692):​n.330+62108G>A variant causes a intron, non coding transcript 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 NR_046198.3 intron, non_coding_transcript
• 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/exons	MANE	UniProt
LINC01692	NR_046198.3	n.330+62108G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01692	ENST00000441009.1	n.330+62108G>A		intron_variant, non_coding_transcript_variant		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;