rs2155304

Variant names:

• chr11-134836049-T-C
• rs2155304
• ENST00000736257.1:n.295+975T>C

Variant summary

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

The ENST00000736257.1(LINC02714):​n.295+975T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,930 control chromosomes in the GnomAD database, including 11,538 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 0.38 (11538 hom., cov: 32)
• Consequence: LINC02714 ENST00000736257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 2 publications found

Genes affected

LINC02714 (HGNC:54231): (long intergenic non-protein coding RNA 2714)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 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
LINC02714	ENST00000736257.1	n.295+975T>C		intron_variant	Intron 2 of 2
LINC02714	ENST00000736258.1	n.295+975T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58311 AN: 151812 Hom.: 11502 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.384 AC: 58401 AN: 151930 Hom.: 11538 Cov.: 32 AF XY: 0.378 AC XY: 28037 AN XY: 74256

African (AFR) AF: 0.455 AC: 18847 AN: 41402

American (AMR) AF: 0.411 AC: 6281 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3472

East Asian (EAS) AF: 0.387 AC: 1989 AN: 5136

South Asian (SAS) AF: 0.309 AC: 1489 AN: 4812

European-Finnish (FIN) AF: 0.216 AC: 2290 AN: 10582

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24476 AN: 67948

Other (OTH) AF: 0.424 AC: 892 AN: 2106

Alfa AF: 0.380 Hom.: 33205

Bravo AF: 0.405

Asia WGS AF: 0.331 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2155304; hg19: chr11-134705943;