rs2351061

Variant names:

• chr11-15679072-T-A
• rs2351061
• ENST00000532242.2:n.366-25261T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-15679072-T-A
• chr11-15679072-T-C

Variant summary

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

The ENST00000532242.2(LINC02751):​n.366-25261T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,484 control chromosomes in the GnomAD database, including 6,436 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 0.29 (6436 hom., cov: 33)
• Consequence: LINC02751 ENST00000532242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 2 publications found

Genes affected

LINC02751 (HGNC:54271): (long intergenic non-protein coding RNA 2751)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02751	NR_169502.1	n.757-25261T>A		intron_variant	Intron 4 of 5
LINC02751	NR_169503.1	n.771-25261T>A		intron_variant	Intron 4 of 5
LINC02751	NR_169507.1	n.84-25261T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02751	ENST00000532242.2	n.366-25261T>A		intron_variant	Intron 2 of 3	3
LINC02751	ENST00000717917.1	n.768-25266T>A		intron_variant	Intron 2 of 3
LINC02751	ENST00000717918.1	n.767-25261T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43304 AN: 151364 Hom.: 6403 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.286 AC: 43389 AN: 151484 Hom.: 6436 Cov.: 33 AF XY: 0.293 AC XY: 21702 AN XY: 74056

African (AFR) AF: 0.289 AC: 11980 AN: 41442

American (AMR) AF: 0.382 AC: 5818 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2174 AN: 5154

South Asian (SAS) AF: 0.314 AC: 1512 AN: 4814

European-Finnish (FIN) AF: 0.285 AC: 3004 AN: 10552

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17273 AN: 67516

Other (OTH) AF: 0.282 AC: 592 AN: 2102

Alfa AF: 0.270 Hom.: 708

Bravo AF: 0.290

Asia WGS AF: 0.352 AC: 1220 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.64
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2351061; hg19: chr11-15700618;