6-26008032-T-C

Variant names:

• chr6-26008032-T-C
• rs9393681
• ENST00000730115.1:n.561+9747T>C

Variant summary

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

The ENST00000730115.1(LINC02980):​n.561+9747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,088 control chromosomes in the GnomAD database, including 13,492 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 0.41 (13492 hom., cov: 32)
• Consequence: LINC02980 ENST00000730115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 17 publications found

Genes affected

LINC02980 (HGNC:56046): (long intergenic non-protein coding RNA 2980)

ENSG00000272558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730115.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02980	ENST00000730115.1		n.561+9747T>C		intron	N/A
	LINC02980	ENST00000730116.1		n.486+9747T>C		intron	N/A
	LINC02980	ENST00000730117.1		n.576-6514T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61579 AN: 151970 Hom.: 13491 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.405 AC: 61602 AN: 152088 Hom.: 13492 Cov.: 32 AF XY: 0.414 AC XY: 30786 AN XY: 74342

African (AFR) AF: 0.263 AC: 10899 AN: 41484

American (AMR) AF: 0.437 AC: 6674 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1292 AN: 3468

East Asian (EAS) AF: 0.751 AC: 3883 AN: 5170

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4820

European-Finnish (FIN) AF: 0.560 AC: 5914 AN: 10568

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29478 AN: 67978

Other (OTH) AF: 0.410 AC: 866 AN: 2110

Alfa AF: 0.421 Hom.: 20223

Bravo AF: 0.393

Asia WGS AF: 0.541 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9393681; hg19: chr6-26008260;