11-28866219-T-C

Variant names:

• chr11-28866219-T-C
• rs11604366
• ENST00000513853.6:n.304+124311T>C

Variant summary

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

The ENST00000513853.6(LINC02742):​n.304+124311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,036 control chromosomes in the GnomAD database, including 10,517 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 0.36 (10517 hom., cov: 32)
• Consequence: LINC02742 ENST00000513853.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 1 publications found

Genes affected

LINC02742 (HGNC:54259): (long intergenic non-protein coding RNA 2742)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513853.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02742	ENST00000513853.6	TSL:3	n.304+124311T>C		intron	N/A
	LINC02742	ENST00000662190.1		n.313-16970T>C		intron	N/A
	LINC02742	ENST00000788052.1		n.295-50662T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54795 AN: 151918 Hom.: 10504 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.361 AC: 54850 AN: 152036 Hom.: 10517 Cov.: 32 AF XY: 0.353 AC XY: 26263 AN XY: 74310

African (AFR) AF: 0.247 AC: 10258 AN: 41480

American (AMR) AF: 0.410 AC: 6256 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5146

South Asian (SAS) AF: 0.276 AC: 1330 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3193 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29204 AN: 67980

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.415 Hom.: 56951

Bravo AF: 0.370

Asia WGS AF: 0.350 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.79
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs11604366; hg19: chr11-28887766;