chr11-78426005-T-C

Variant names:

• chr11-78426005-T-C
• rs34956708
• ENST00000513207.2:n.360-600A>G

Variant summary

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

The ENST00000513207.2(LINC02728):​n.360-600A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 152,290 control chromosomes in the GnomAD database, including 379 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 0.056 (379 hom., cov: 32)
• Consequence: LINC02728 ENST00000513207.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 1 publications found

Genes affected

LINC02728 (HGNC:54245): (long intergenic non-protein coding RNA 2728)

ENSG00000288853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513207.2. 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
	LINC02728	NR_120564.1		n.360-600A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02728	ENST00000513207.2	TSL:1	n.360-600A>G		intron	N/A
	LINC02728	ENST00000660634.1		n.659-600A>G		intron	N/A
	LINC02728	ENST00000664831.1		n.503-600A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0560 AC: 8520 AN: 152172 Hom.: 378 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0799

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0560 AC: 8521 AN: 152290 Hom.: 379 Cov.: 32 AF XY: 0.0562 AC XY: 4185 AN XY: 74464

African (AFR) AF: 0.0134 AC: 557 AN: 41580

American (AMR) AF: 0.0461 AC: 705 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0468 AC: 226 AN: 4826

European-Finnish (FIN) AF: 0.0997 AC: 1056 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0799 AC: 5437 AN: 68018

Other (OTH) AF: 0.0501 AC: 106 AN: 2116

Alfa AF: 0.0566 Hom.: 289

Bravo AF: 0.0509

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs34956708; hg19: chr11-78137051;