11-123313261-C-T

Variant names:

• chr11-123313261-C-T
• rs10893006
• ENST00000729378.1:n.281+1242G>A

Variant summary

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

The ENST00000729378.1(LINC02727):​n.281+1242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,108 control chromosomes in the GnomAD database, including 23,849 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 0.51 (23849 hom., cov: 32)
• Consequence: LINC02727 ENST00000729378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.03
• Publications: 4 publications found

Genes affected

LINC02727 (HGNC:54244): (long intergenic non-protein coding RNA 2727)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02727	ENST00000729378.1	n.281+1242G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77359 AN: 151990 Hom.: 23788 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.509 AC: 77486 AN: 152108 Hom.: 23849 Cov.: 32 AF XY: 0.505 AC XY: 37580 AN XY: 74360

African (AFR) AF: 0.875 AC: 36347 AN: 41522

American (AMR) AF: 0.448 AC: 6838 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3466

East Asian (EAS) AF: 0.470 AC: 2432 AN: 5176

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4079 AN: 10566

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23482 AN: 67960

Other (OTH) AF: 0.458 AC: 969 AN: 2114

Alfa AF: 0.389 Hom.: 7148

Bravo AF: 0.530

Asia WGS AF: 0.425 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.086
DANN	Benign	0.49
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs10893006; hg19: chr11-123183969;