rs1531903

Variant names:

• chr11-15647280-C-G
• rs1531903
• ENST00000532242.2:n.365+3245C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-15647280-C-G
• chr11-15647280-C-T

Variant summary

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

The ENST00000532242.2(LINC02751):​n.365+3245C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,172 control chromosomes in the GnomAD database, including 45,459 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 0.77 (45459 hom., cov: 32)
• Consequence: LINC02751 ENST00000532242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 7 publications found

Genes affected

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

ENSG00000295117 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02751	NR_169502.1	n.756+3245C>G		intron_variant	Intron 4 of 5
LINC02751	NR_169503.1	n.770+3245C>G		intron_variant	Intron 4 of 5
LINC02751	NR_169507.1	n.83+23093C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02751	ENST00000532242.2	n.365+3245C>G		intron_variant	Intron 2 of 3	3
LINC02751	ENST00000717917.1	n.768-57058C>G		intron_variant	Intron 2 of 3
LINC02751	ENST00000717918.1	n.767-57053C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117023 AN: 152054 Hom.: 45422 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.770 AC: 117111 AN: 152172 Hom.: 45459 Cov.: 32 AF XY: 0.766 AC XY: 56961 AN XY: 74380

African (AFR) AF: 0.696 AC: 28867 AN: 41502

American (AMR) AF: 0.790 AC: 12075 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2574 AN: 3470

East Asian (EAS) AF: 0.780 AC: 4024 AN: 5160

South Asian (SAS) AF: 0.873 AC: 4212 AN: 4824

European-Finnish (FIN) AF: 0.642 AC: 6801 AN: 10590

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 56009 AN: 68016

Other (OTH) AF: 0.769 AC: 1628 AN: 2116

Alfa AF: 0.737 Hom.: 2238

Bravo AF: 0.772

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.073
DANN	Benign	0.32
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1531903; hg19: chr11-15668826;