rs898309

Variant names:

• chr11-112754370-A-G
• rs898309
• ENST00000688876.1:n.585-6810A>G

Variant summary

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

The ENST00000688876.1(LINC02763):​n.585-6810A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,996 control chromosomes in the GnomAD database, including 32,876 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 0.64 (32876 hom., cov: 32)
• Consequence: LINC02763 ENST00000688876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 2 publications found

Genes affected

LINC02763 (HGNC:54282): (long intergenic non-protein coding RNA 2763)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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
LINC02763	ENST00000688876.1	n.585-6810A>G		intron_variant	Intron 3 of 3
LINC02763	ENST00000691666.2	n.690-6810A>G		intron_variant	Intron 4 of 4
LINC02763	ENST00000763471.1	n.344-14072A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97394 AN: 151876 Hom.: 32859 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.641 AC: 97464 AN: 151996 Hom.: 32876 Cov.: 32 AF XY: 0.636 AC XY: 47259 AN XY: 74294

African (AFR) AF: 0.432 AC: 17902 AN: 41426

American (AMR) AF: 0.677 AC: 10337 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2591 AN: 3472

East Asian (EAS) AF: 0.463 AC: 2386 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2733 AN: 4818

European-Finnish (FIN) AF: 0.677 AC: 7146 AN: 10560

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52073 AN: 67978

Other (OTH) AF: 0.681 AC: 1435 AN: 2108

Alfa AF: 0.729 Hom.: 20781

Bravo AF: 0.635

Asia WGS AF: 0.543 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.64
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs898309; hg19: chr11-112625093;