rs9982805

Variant names:

• chr21-22011290-C-A
• rs9982805
• ENST00000420255.1:n.697-1932G>T

Your query was ambiguous. Multiple possible variants found:

• chr21-22011290-C-A
• chr21-22011290-C-T

Variant summary

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

The ENST00000420255.1(LINC01687):​n.697-1932G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,154 control chromosomes in the GnomAD database, including 282 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 0.052 (282 hom., cov: 32)
• Consequence: LINC01687 ENST00000420255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

Genes affected

LINC01687 (HGNC:52474): (long intergenic non-protein coding RNA 1687)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420255.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01687	NR_109959.1		n.697-1932G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01687	ENST00000420255.1	TSL:1	n.697-1932G>T		intron	N/A
	LINC01687	ENST00000416327.5	TSL:3	n.381-1932G>T		intron	N/A
	LINC01687	ENST00000667392.1		n.756-1932G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7893 AN: 152036 Hom.: 281 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00953

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0519 AC: 7904 AN: 152154 Hom.: 282 Cov.: 32 AF XY: 0.0505 AC XY: 3759 AN XY: 74394

African (AFR) AF: 0.108 AC: 4492 AN: 41506

American (AMR) AF: 0.0226 AC: 346 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 63 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.00954 AC: 46 AN: 4822

European-Finnish (FIN) AF: 0.0412 AC: 436 AN: 10590

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2381 AN: 68008

Other (OTH) AF: 0.0433 AC: 91 AN: 2102

Alfa AF: 0.0379 Hom.: 212

Bravo AF: 0.0543

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.46
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9982805;

hg19: chr21-23383609;