rs6984050

Variant names:

• chr8-126251757-A-C
• rs6984050
• ENST00000651482.1:n.198+40834T>G

Variant summary

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

The ENST00000651482.1(LINC00861):​n.198+40834T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,048 control chromosomes in the GnomAD database, including 4,857 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 0.25 (4857 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 1 publications found

Genes affected

LINC00861 (HGNC:45133): (long intergenic non-protein coding RNA 861)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 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
LINC00861	ENST00000651482.1	n.198+40834T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38030 AN: 151930 Hom.: 4855 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.250 AC: 38040 AN: 152048 Hom.: 4857 Cov.: 32 AF XY: 0.251 AC XY: 18682 AN XY: 74328

African (AFR) AF: 0.199 AC: 8256 AN: 41472

American (AMR) AF: 0.240 AC: 3662 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1563 AN: 5170

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4814

European-Finnish (FIN) AF: 0.275 AC: 2901 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18430 AN: 67970

Other (OTH) AF: 0.253 AC: 535 AN: 2116

Alfa AF: 0.247 Hom.: 1973

Bravo AF: 0.241

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.84
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6984050; hg19: chr8-127264002;