rs6587361

Variant names:

• chr1-229883301-G-A
• rs6587361
• ENST00000435973.3:n.400+2239C>T

Variant summary

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

The ENST00000435973.3(LINC01682):​n.400+2239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,246 control chromosomes in the GnomAD database, including 10,878 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 0.21 (10878 hom., cov: 33)
• Consequence: LINC01682 ENST00000435973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 8 publications found

Genes affected

LINC01682 (HGNC:52470): (long intergenic non-protein coding RNA 1682)

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 = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435973.3. 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
	LINC01682	NR_146476.1		n.279+2239C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01682	ENST00000435973.3	TSL:2	n.400+2239C>T		intron	N/A
	LINC01682	ENST00000650825.1		n.44-7580C>T		intron	N/A
	LINC01682	ENST00000661713.1		n.335+2239C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31584 AN: 152128 Hom.: 10849 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00456

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.208 AC: 31661 AN: 152246 Hom.: 10878 Cov.: 33 AF XY: 0.201 AC XY: 14937 AN XY: 74450

African (AFR) AF: 0.715 AC: 29655 AN: 41494

American (AMR) AF: 0.0832 AC: 1274 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00789 AC: 38 AN: 4816

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.00454 AC: 309 AN: 68032

Other (OTH) AF: 0.151 AC: 319 AN: 2116

Alfa AF: 0.0936 Hom.: 784

Bravo AF: 0.238

Asia WGS AF: 0.0530 AC: 185 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	0.40
DANN	Benign	0.42
PhyloP100		-0.52
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: rs6587361; hg19: chr1-230019048;