chr11-134756993-T-C

Variant names:

• chr11-134756993-T-C
• rs11223996
• ENST00000513405.1:n.948-4081T>C

Variant summary

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

The ENST00000513405.1(LINC02714):​n.948-4081T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,220 control chromosomes in the GnomAD database, including 974 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 0.11 (974 hom., cov: 33)
• Consequence: LINC02714 ENST00000513405.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02714	NR_147836.1	n.599-4081T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02714	ENST00000513405.1	n.948-4081T>C		intron_variant	Intron 1 of 1	2
LINC02714	ENST00000809938.1	n.147-4076T>C		intron_variant	Intron 1 of 1
LINC02714	ENST00000809939.1	n.183-4076T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16518 AN: 152102 Hom.: 972 Cov.: 33

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.109 AC: 16527 AN: 152220 Hom.: 974 Cov.: 33 AF XY: 0.108 AC XY: 8059 AN XY: 74426

African (AFR) AF: 0.0697 AC: 2894 AN: 41534

American (AMR) AF: 0.159 AC: 2430 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.0944 AC: 488 AN: 5170

South Asian (SAS) AF: 0.0508 AC: 245 AN: 4826

European-Finnish (FIN) AF: 0.0966 AC: 1024 AN: 10600

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8472 AN: 68010

Other (OTH) AF: 0.139 AC: 294 AN: 2108

Alfa AF: 0.122 Hom.: 3738

Bravo AF: 0.116

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.41
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs11223996; hg19: chr11-134626887;