rs6517502

chr21-39020677-G-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02940	ENST00000652155.1	n.351-2896C>A		intron_variant, non_coding_transcript_variant

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;