rs1531903

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_169502.1(LINC02751):​n.756+3245C>G variant causes a intron, non coding transcript 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 NR_169502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02751	NR_169502.1	n.756+3245C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000532242.2	n.365+3245C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.769

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531903; hg19: chr11-15668826;