chr6-106697506-T-G

Position:

• chr6-106697506-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424162.1(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 ENST00000424162.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

LINC02526 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02526	NR_149100.1	n.316+1106T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02526	ENST00000424162.1	n.266+1106T>G		intron_variant		2

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

Gnomad4 AFR AF: 0.00491

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0369

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485221; hg19: chr6-107145381;