rs9982805

chr21-22011290-C-Achr21-22011290-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109959.1(LINC01687):n.697-1932G>T variant causes a intron, non coding transcript 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 NR_109959.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01687	NR_109959.1	n.697-1932G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01687	ENST00000420255.1	n.697-1932G>T		intron_variant, non_coding_transcript_variant		1
LINC01687	ENST00000669715.1	n.856-1932G>T		intron_variant, non_coding_transcript_variant
LINC01687	ENST00000416327.5	n.381-1932G>T		intron_variant, non_coding_transcript_variant		3
LINC01687	ENST00000667392.1	n.756-1932G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0181

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00954

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0433

Alfa AF: 0.0349 Hom.: 132

Bravo AF: 0.0543

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.47
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9982805; hg19: chr21-23383609;