11-17652683-T-C

Variant names:

• chr11-17652683-T-C
• rs3935159
• ENST00000849122.1:n.105-6156A>G

Variant summary

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

The ENST00000849122.1(LINC02729):​n.105-6156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,008 control chromosomes in the GnomAD database, including 27,457 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 0.57 (27457 hom., cov: 32)
• Consequence: LINC02729 ENST00000849122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.985
• Publications: 5 publications found

Genes affected

LINC02729 (HGNC:54246): (long intergenic non-protein coding RNA 2729)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02729	ENST00000849122.1	n.105-6156A>G		intron_variant	Intron 1 of 2
LINC02729	ENST00000849123.1	n.138-1250A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85981 AN: 151890 Hom.: 27463 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.566 AC: 85988 AN: 152008 Hom.: 27457 Cov.: 32 AF XY: 0.570 AC XY: 42358 AN XY: 74294

African (AFR) AF: 0.253 AC: 10484 AN: 41442

American (AMR) AF: 0.640 AC: 9775 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2586 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4657 AN: 5160

South Asian (SAS) AF: 0.573 AC: 2755 AN: 4810

European-Finnish (FIN) AF: 0.718 AC: 7597 AN: 10584

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46074 AN: 67956

Other (OTH) AF: 0.602 AC: 1267 AN: 2106

Alfa AF: 0.615 Hom.: 5096

Bravo AF: 0.552

Asia WGS AF: 0.696 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs3935159; hg19: chr11-17674230;