ENST00000570443.2:n.357+11564T>C

Variant names:

• chr6-37519268-T-C
• rs1757171
• ENST00000570443.2:n.357+11564T>C

Variant summary

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

The ENST00000570443.2(LINC02520):​n.357+11564T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,134 control chromosomes in the GnomAD database, including 28,553 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 0.61 (28553 hom., cov: 33)
• Consequence: LINC02520 ENST00000570443.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 21 publications found

Genes affected

LINC02520 (HGNC:53511): (long intergenic non-protein coding RNA 2520)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000570443.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02520	NR_126057.1		n.357+11564T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02520	ENST00000570443.2	TSL:4	n.357+11564T>C		intron	N/A
	LINC02520	ENST00000689244.2		n.230+2327T>C		intron	N/A
	LINC02520	ENST00000690655.2		n.230+2327T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92065 AN: 152016 Hom.: 28538 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.606 AC: 92118 AN: 152134 Hom.: 28553 Cov.: 33 AF XY: 0.598 AC XY: 44493 AN XY: 74368

African (AFR) AF: 0.531 AC: 22017 AN: 41468

American (AMR) AF: 0.660 AC: 10106 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2481 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1528 AN: 5182

South Asian (SAS) AF: 0.549 AC: 2648 AN: 4826

European-Finnish (FIN) AF: 0.586 AC: 6203 AN: 10590

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44928 AN: 67980

Other (OTH) AF: 0.617 AC: 1301 AN: 2110

Alfa AF: 0.643 Hom.: 111075

Bravo AF: 0.607

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1757171; hg19: chr6-37487044;