chr6-37543156-G-T

Variant names:

• chr6-37543156-G-T
• rs2797777
• ENST00000829675.1:n.275-5890G>T

Variant summary

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

The ENST00000829675.1(LINC02520):​n.275-5890G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,118 control chromosomes in the GnomAD database, including 44,512 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 0.76 (44512 hom., cov: 33)
• Consequence: LINC02520 ENST00000829675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829675.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02520	ENST00000829675.1		n.275-5890G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115640 AN: 151998 Hom.: 44474 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.761 AC: 115724 AN: 152118 Hom.: 44512 Cov.: 33 AF XY: 0.758 AC XY: 56348 AN XY: 74362

African (AFR) AF: 0.802 AC: 33271 AN: 41500

American (AMR) AF: 0.810 AC: 12386 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2943 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1885 AN: 5168

South Asian (SAS) AF: 0.694 AC: 3347 AN: 4824

European-Finnish (FIN) AF: 0.706 AC: 7463 AN: 10572

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51862 AN: 67986

Other (OTH) AF: 0.763 AC: 1607 AN: 2106

Alfa AF: 0.764 Hom.: 146673

Bravo AF: 0.770

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.75
DANN	Benign	0.50
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2797777; hg19: chr6-37510932;