rs6517502

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652155.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02940	ENST00000652155.1		n.351-2896C>A		intron	N/A
	LINC02940	ENST00000809871.1		n.79+593C>A		intron	N/A

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

African (AFR) AF: 0.722 AC: 29902 AN: 41434

American (AMR) AF: 0.654 AC: 9988 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2884 AN: 5144

South Asian (SAS) AF: 0.610 AC: 2938 AN: 4816

European-Finnish (FIN) AF: 0.510 AC: 5374 AN: 10534

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40028 AN: 67966

Other (OTH) AF: 0.642 AC: 1355 AN: 2110

Alfa AF: 0.611 Hom.: 53185

Bravo AF: 0.644

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.50
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs6517502; hg19: chr21-40392603;