rs2076848

Variant names:

• chr11-134797652-A-T
• rs2076848
• ENST00000701514.2:n.354-5552A>T

Variant summary

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

The ENST00000701514.2(LINC02714):​n.354-5552A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,060 control chromosomes in the GnomAD database, including 10,325 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 0.35 (10325 hom., cov: 33)
• Consequence: LINC02714 ENST00000701514.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 16 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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	ENST00000701514.2	n.354-5552A>T		intron_variant	Intron 1 of 4
LINC02714	ENST00000736257.1	n.177+34928A>T		intron_variant	Intron 1 of 2
LINC02714	ENST00000736258.1	n.177+34928A>T		intron_variant	Intron 1 of 2
LINC02714	ENST00000736259.1	n.355-4507A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53627 AN: 151942 Hom.: 10334 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.353 AC: 53620 AN: 152060 Hom.: 10325 Cov.: 33 AF XY: 0.346 AC XY: 25739 AN XY: 74322

African (AFR) AF: 0.207 AC: 8579 AN: 41488

American (AMR) AF: 0.327 AC: 4996 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1856 AN: 5170

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 3000 AN: 10576

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29827 AN: 67952

Other (OTH) AF: 0.398 AC: 840 AN: 2112

Alfa AF: 0.378 Hom.: 1424

Bravo AF: 0.351

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2076848; hg19: chr11-134667546;