8-65551243-G-T

Variant names:

• chr8-65551243-G-T
• rs6981992
• ENST00000520902.2:n.176+11363C>A

Variant summary

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

The ENST00000520902.2(LINC01299):​n.176+11363C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,900 control chromosomes in the GnomAD database, including 40,935 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 0.71 (40935 hom., cov: 32)
• Consequence: LINC01299 ENST00000520902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 9 publications found

Genes affected

LINC01299 (HGNC:27839): (long intergenic non-protein coding RNA 1299)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01299	NR_033893.1	n.61+11363C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01299	ENST00000520902.2	n.176+11363C>A		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108258 AN: 151782 Hom.: 40892 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.713 AC: 108363 AN: 151900 Hom.: 40935 Cov.: 32 AF XY: 0.695 AC XY: 51599 AN XY: 74218

African (AFR) AF: 0.897 AC: 37213 AN: 41484

American (AMR) AF: 0.573 AC: 8745 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2516 AN: 3466

East Asian (EAS) AF: 0.0940 AC: 486 AN: 5168

South Asian (SAS) AF: 0.375 AC: 1806 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6449 AN: 10490

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48825 AN: 67904

Other (OTH) AF: 0.695 AC: 1468 AN: 2112

Alfa AF: 0.710 Hom.: 86212

Bravo AF: 0.720

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.52
DANN	Benign	0.35
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs6981992; hg19: chr8-66463478;