rs6517502

Variant names:

• chr21-39020677-G-T
• rs6517502
• ENST00000652155.1:n.351-2896C>A

Variant summary

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

The ENST00000652155.1(LINC02940):​n.351-2896C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,952 control chromosomes in the GnomAD database, including 30,370 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 0.63 (30370 hom., cov: 31)
• Consequence: LINC02940 ENST00000652155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

Genes affected

LINC02940 (HGNC:55955): (long intergenic non-protein coding RNA 2940)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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
LINC02940	ENST00000652155.1	n.351-2896C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95206 AN: 151834 Hom.: 30318 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.627 AC: 95314 AN: 151952 Hom.: 30370 Cov.: 31 AF XY: 0.622 AC XY: 46131 AN XY: 74216

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.642

Alfa AF: 0.612 Hom.: 13685

Bravo AF: 0.644

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6517502; hg19: chr21-40392603;