rs8106239

Variant names:

• chr19-35594456-A-C
• rs8106239
• ENST00000716278.1:n.323-6185A>C

Variant summary

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

The ENST00000716278.1(LINC01766):​n.323-6185A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,034 control chromosomes in the GnomAD database, including 4,245 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 0.23 (4245 hom., cov: 31)
• Consequence: LINC01766 ENST00000716278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 2 publications found

Genes affected

LINC01766 (HGNC:52556): (long intergenic non-protein coding RNA 1766)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716278.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01766	ENST00000716278.1		n.323-6185A>C		intron	N/A
	LINC01766	ENST00000716279.1		n.200-6185A>C		intron	N/A
	LINC01766	ENST00000841208.1		n.179-6185A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34925 AN: 151916 Hom.: 4245 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.230 AC: 34930 AN: 152034 Hom.: 4245 Cov.: 31 AF XY: 0.226 AC XY: 16773 AN XY: 74318

African (AFR) AF: 0.236 AC: 9781 AN: 41448

American (AMR) AF: 0.323 AC: 4934 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1735 AN: 5168

South Asian (SAS) AF: 0.0757 AC: 365 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1498 AN: 10580

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15399 AN: 67974

Other (OTH) AF: 0.238 AC: 501 AN: 2108

Alfa AF: 0.215 Hom.: 1824

Bravo AF: 0.249

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs8106239; hg19: chr19-36085358;