rs11223996

Positions:

• chr11-134756993-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147836.1(LINC02714):​n.599-4081T>C variant causes a intron, non coding transcript 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 NR_147836.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02714	NR_147836.1	n.599-4081T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02714	ENST00000513405.1	n.948-4081T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0944

Gnomad4 SAS AF: 0.0508

Gnomad4 FIN AF: 0.0966

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.139

Alfa AF: 0.128 Hom.: 1732

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11223996; hg19: chr11-134626887;