rs10485221

Variant names:

• chr6-106697506-T-G
• rs10485221
• ENST00000424162.2:n.266+1106T>G

Variant summary

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

The ENST00000424162.2(LINC02526):​n.266+1106T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 152,326 control chromosomes in the GnomAD database, including 289 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 0.034 (289 hom., cov: 33)
• Consequence: LINC02526 ENST00000424162.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 2 publications found

Genes affected

LINC02526 (HGNC:53550): (long intergenic non-protein coding RNA 2526)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424162.2. 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
	LINC02526	NR_149100.1		n.316+1106T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02526	ENST00000424162.2	TSL:2	n.266+1106T>G		intron	N/A
	LINC02526	ENST00000771592.1		n.632+1106T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0344 AC: 5239 AN: 152208 Hom.: 285 Cov.: 33

Gnomad AFR AF: 0.00492

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0377

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

GnomAD4 genome AF: 0.0345 AC: 5248 AN: 152326 Hom.: 289 Cov.: 33 AF XY: 0.0400 AC XY: 2983 AN XY: 74496

African (AFR) AF: 0.00491 AC: 204 AN: 41580

American (AMR) AF: 0.113 AC: 1729 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1091 AN: 5182

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4828

European-Finnish (FIN) AF: 0.104 AC: 1108 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 887 AN: 68032

Other (OTH) AF: 0.0369 AC: 78 AN: 2116

Alfa AF: 0.0276 Hom.: 30

Bravo AF: 0.0366

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.64

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: rs10485221;

hg19: chr6-107145381;