11-127334069-T-C

Variant names:

• chr11-127334069-T-C
• rs2697717
• ENST00000608214.3:n.144-955T>C

Variant summary

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

The ENST00000608214.3(LINC02712):​n.144-955T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,096 control chromosomes in the GnomAD database, including 1,722 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 0.13 (1722 hom., cov: 32)
• Consequence: LINC02712 ENST00000608214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 4 publications found

Genes affected

LINC02712 (HGNC:54229): (long intergenic non-protein coding RNA 2712)

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 = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02712	NR_120580.1		n.105-955T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02712	ENST00000608214.3	TSL:1	n.144-955T>C		intron	N/A
	LINC02712	ENST00000748492.1		n.73-955T>C		intron	N/A
	LINC02712	ENST00000748493.1		n.143-955T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19846 AN: 151978 Hom.: 1718 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.131 AC: 19853 AN: 152096 Hom.: 1722 Cov.: 32 AF XY: 0.131 AC XY: 9763 AN XY: 74354

African (AFR) AF: 0.230 AC: 9541 AN: 41428

American (AMR) AF: 0.0865 AC: 1322 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.174 AC: 900 AN: 5172

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4822

European-Finnish (FIN) AF: 0.0748 AC: 793 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0788 AC: 5357 AN: 68000

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.0861 Hom.: 1004

Bravo AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.84
DANN	Benign	0.38
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2697717; hg19: chr11-127203964;