rs13251380

Variant names:

• chr8-126280186-C-T
• rs13251380
• ENST00000651482.1:n.198+12405G>A

Variant summary

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

The ENST00000651482.1(LINC00861):​n.198+12405G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,040 control chromosomes in the GnomAD database, including 6,121 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 0.28 (6121 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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+12405G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42969 AN: 151920 Hom.: 6112 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.283 AC: 42997 AN: 152040 Hom.: 6121 Cov.: 32 AF XY: 0.283 AC XY: 21031 AN XY: 74294

African (AFR) AF: 0.309 AC: 12804 AN: 41456

American (AMR) AF: 0.252 AC: 3859 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1545 AN: 5154

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2895 AN: 10560

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18591 AN: 67978

Other (OTH) AF: 0.278 AC: 588 AN: 2112

Alfa AF: 0.265 Hom.: 933

Bravo AF: 0.278

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.52
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs13251380; hg19: chr8-127292431;