rs10091374

Variant names:

• chr8-70474669-T-A
• rs10091374
• ENST00000520259.1:n.712+2824T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-70474669-T-A
• chr8-70474669-T-C

Variant summary

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

The ENST00000520259.1(LINC03020):​n.712+2824T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,854 control chromosomes in the GnomAD database, including 16,888 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 0.47 (16888 hom., cov: 31)
• Consequence: LINC03020 ENST00000520259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 14 publications found

Genes affected

LINC03020 (HGNC:56148): (long intergenic non-protein coding RNA 3020)

ENSG00000253143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520259.1. 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
	LINC03020	NR_110653.1		n.712+2824T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03020	ENST00000520259.1	TSL:2	n.712+2824T>A		intron	N/A
	ENSG00000253143	ENST00000521051.1	TSL:5	n.704-3525A>T		intron	N/A
	LINC03020	ENST00000757201.1		n.800+2824T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70702 AN: 151736 Hom.: 16855 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.466 AC: 70794 AN: 151854 Hom.: 16888 Cov.: 31 AF XY: 0.464 AC XY: 34449 AN XY: 74222

African (AFR) AF: 0.451 AC: 18652 AN: 41372

American (AMR) AF: 0.357 AC: 5449 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3466

East Asian (EAS) AF: 0.664 AC: 3433 AN: 5172

South Asian (SAS) AF: 0.375 AC: 1806 AN: 4820

European-Finnish (FIN) AF: 0.504 AC: 5297 AN: 10520

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33380 AN: 67930

Other (OTH) AF: 0.457 AC: 961 AN: 2104

Alfa AF: 0.478 Hom.: 2154

Bravo AF: 0.458

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.27
PhyloP100		0.13

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: rs10091374;

hg19: chr8-71386904;