11-11175086-T-A

Position:

• chr11-11175086-T-A

Variant summary

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

The ENST00000525758.1(LINC02752):​n.562-4821T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,152 control chromosomes in the GnomAD database, including 6,047 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 0.27 (6047 hom., cov: 33)
• Consequence: LINC02752 ENST00000525758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972

Genes affected

LINC02752 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02752	NR_187402.1	n.677-4821T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000525758.1	n.562-4821T>A		intron_variant		1
LINC02752	ENST00000647635.1	n.391-4821T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41398 AN: 152034 Hom.: 6048 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.272 AC: 41416 AN: 152152 Hom.: 6047 Cov.: 33 AF XY: 0.269 AC XY: 20045 AN XY: 74412

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.324

Alfa AF: 0.284 Hom.: 794

Bravo AF: 0.275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	17
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4910266; hg19: chr11-11196633;