1-208636753-C-T

Variant summary

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

The XR_007066853.1(LINC02769):n.2251G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,994 control chromosomes in the GnomAD database, including 23,655 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 0.56 (23655 hom., cov: 32)
• Consequence: LINC02769 XR_007066853.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

Genes affected

LINC02769 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02769	XR_007066853.1	n.2251G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84564 AN: 151876 Hom.: 23625 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.557 AC: 84636 AN: 151994 Hom.: 23655 Cov.: 32 AF XY: 0.561 AC XY: 41697 AN XY: 74292

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.540

Alfa AF: 0.532 Hom.: 20824

Bravo AF: 0.561

Asia WGS AF: 0.558 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.1
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1166864; hg19: chr1-208810098;