rs10094775

Variant names:

• chr8-126185310-G-A
• rs10094775
• ENST00000651482.1:n.199-72229C>T

Variant summary

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

The ENST00000651482.1(LINC00861):​n.199-72229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,968 control chromosomes in the GnomAD database, including 12,551 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 0.39 (12551 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651482.1. 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
	LINC00861	ENST00000651482.1		n.199-72229C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58655 AN: 151850 Hom.: 12529 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.386 AC: 58731 AN: 151968 Hom.: 12551 Cov.: 32 AF XY: 0.385 AC XY: 28608 AN XY: 74286

African (AFR) AF: 0.585 AC: 24270 AN: 41452

American (AMR) AF: 0.385 AC: 5874 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5162

South Asian (SAS) AF: 0.296 AC: 1424 AN: 4816

European-Finnish (FIN) AF: 0.325 AC: 3427 AN: 10558

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19845 AN: 67930

Other (OTH) AF: 0.352 AC: 742 AN: 2110

Alfa AF: 0.314 Hom.: 4143

Bravo AF: 0.402

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.74
DANN	Benign	0.24
PhyloP100		0.041

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10094775;

hg19: chr8-127197554;