rs8086768

Variant names:

• chr18-22058349-T-A
• rs8086768
• ENST00000716236.1:n.347+14497T>A

Variant summary

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

The ENST00000716236.1(LINC01900):​n.347+14497T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,084 control chromosomes in the GnomAD database, including 2,694 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 0.17 (2694 hom., cov: 31)
• Consequence: LINC01900 ENST00000716236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

LINC01900 (HGNC:52719): (long intergenic non-protein coding RNA 1900)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716236.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01900	ENST00000716236.1		n.347+14497T>A		intron	N/A
	LINC01900	ENST00000780669.1		n.348+14497T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25591 AN: 151966 Hom.: 2689 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.168 AC: 25607 AN: 152084 Hom.: 2694 Cov.: 31 AF XY: 0.172 AC XY: 12810 AN XY: 74336

African (AFR) AF: 0.238 AC: 9887 AN: 41476

American (AMR) AF: 0.292 AC: 4461 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5158

South Asian (SAS) AF: 0.203 AC: 979 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1190 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6919 AN: 67998

Other (OTH) AF: 0.167 AC: 353 AN: 2116

Alfa AF: 0.142 Hom.: 217

Bravo AF: 0.185

Asia WGS AF: 0.239 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8086768; hg19: chr18-19638310;