chr8-34843012-A-G

Variant names:

• chr8-34843012-A-G
• rs16883114
• ENST00000519189.2:n.412-21645A>G

Variant summary

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

The ENST00000519189.2(LINC01288):​n.412-21645A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0374 in 151,808 control chromosomes in the GnomAD database, including 585 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 0.037 (585 hom., cov: 32)
• Consequence: LINC01288 ENST00000519189.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.735
• Publications: 5 publications found

Genes affected

LINC01288 (HGNC:50353): (long intergenic non-protein coding RNA 1288)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519189.2. 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
	LINC01288	NR_125746.1		n.519-21645A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01288	ENST00000519189.2	TSL:4	n.412-21645A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5682 AN: 151690 Hom.: 585 Cov.: 32

Gnomad AFR AF: 0.00828

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0480

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0360

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

GnomAD4 genome AF: 0.0374 AC: 5681 AN: 151808 Hom.: 585 Cov.: 32 AF XY: 0.0413 AC XY: 3066 AN XY: 74234

African (AFR) AF: 0.00826 AC: 342 AN: 41402

American (AMR) AF: 0.0504 AC: 768 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0480 AC: 166 AN: 3460

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5150

South Asian (SAS) AF: 0.104 AC: 499 AN: 4810

European-Finnish (FIN) AF: 0.0260 AC: 274 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1291 AN: 67888

Other (OTH) AF: 0.0361 AC: 76 AN: 2106

Alfa AF: 0.0251 Hom.: 211

Bravo AF: 0.0400

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs16883114; hg19: chr8-34700530;