11-123308356-A-C

Variant names:

• chr11-123308356-A-C
• rs9888300
• ENST00000729378.1:n.282-3977T>G

Variant summary

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

The ENST00000729378.1(LINC02727):​n.282-3977T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,050 control chromosomes in the GnomAD database, including 25,536 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 0.54 (25536 hom., cov: 32)
• Consequence: LINC02727 ENST00000729378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

Genes affected

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

ENSG00000295353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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.282-3977T>G		intron_variant	Intron 1 of 2
ENSG00000295353	ENST00000729481.1	n.111+718A>C		intron_variant	Intron 1 of 2
ENSG00000295353	ENST00000729482.1	n.113+718A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81765 AN: 151932 Hom.: 25477 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.539 AC: 81888 AN: 152050 Hom.: 25536 Cov.: 32 AF XY: 0.534 AC XY: 39656 AN XY: 74330

African (AFR) AF: 0.878 AC: 36423 AN: 41488

American (AMR) AF: 0.476 AC: 7274 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2417 AN: 5156

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4384 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26640 AN: 67958

Other (OTH) AF: 0.492 AC: 1036 AN: 2106

Alfa AF: 0.401 Hom.: 7183

Bravo AF: 0.560

Asia WGS AF: 0.431 AC: 1498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.17
DANN	Benign	0.78
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9888300; hg19: chr11-123179064;