rs880275

Variant names:

• chr16-86214171-G-A
• rs880275
• ENST00000806578.1:n.182+17759G>A

Variant summary

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

The ENST00000806578.1(LINC01082):​n.182+17759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,066 control chromosomes in the GnomAD database, including 5,751 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 0.26 (5751 hom., cov: 32)
• Consequence: LINC01082 ENST00000806578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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+17759G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38880 AN: 151948 Hom.: 5756 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.256 AC: 38878 AN: 152066 Hom.: 5751 Cov.: 32 AF XY: 0.256 AC XY: 19060 AN XY: 74318

African (AFR) AF: 0.113 AC: 4673 AN: 41520

American (AMR) AF: 0.260 AC: 3976 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1340 AN: 3458

East Asian (EAS) AF: 0.408 AC: 2102 AN: 5154

South Asian (SAS) AF: 0.221 AC: 1060 AN: 4798

European-Finnish (FIN) AF: 0.334 AC: 3531 AN: 10566

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21197 AN: 67968

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.293 Hom.: 3440

Bravo AF: 0.247

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.86
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs880275; hg19: chr16-86247777;