rs276960

Variant names:

• chr16-86203798-C-T
• rs276960
• ENST00000806578.1:n.182+7386C>T

Variant summary

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

The ENST00000806578.1(LINC01082):​n.182+7386C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,142 control chromosomes in the GnomAD database, including 58,337 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 0.87 (58337 hom., cov: 31)
• Consequence: LINC01082 ENST00000806578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 1 publications found

Genes affected

LINC01082 (HGNC:49125): (long intergenic non-protein coding RNA 1082)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01082	ENST00000806578.1	n.182+7386C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133037 AN: 152024 Hom.: 58303 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.875 AC: 133124 AN: 152142 Hom.: 58337 Cov.: 31 AF XY: 0.874 AC XY: 65011 AN XY: 74380

African (AFR) AF: 0.855 AC: 35452 AN: 41484

American (AMR) AF: 0.881 AC: 13478 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3274 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4716 AN: 5174

South Asian (SAS) AF: 0.723 AC: 3476 AN: 4808

European-Finnish (FIN) AF: 0.931 AC: 9869 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60016 AN: 67994

Other (OTH) AF: 0.883 AC: 1865 AN: 2112

Alfa AF: 0.875 Hom.: 7243

Bravo AF: 0.877

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.41
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs276960; hg19: chr16-86237404;