6-37550405-C-T

Variant names:

• chr6-37550405-C-T
• rs914351
• ENST00000414875.2:n.706-163C>T

Variant summary

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

The ENST00000414875.2(LINC02520):​n.706-163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,252 control chromosomes in the GnomAD database, including 4,403 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 0.23 (4403 hom., cov: 34)
• Consequence: LINC02520 ENST00000414875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 2 publications found

Genes affected

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

ENSG00000309723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414875.2. 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
	LINC02520	ENST00000414875.2	TSL:5	n.706-163C>T		intron	N/A
	LINC02520	ENST00000656831.1		n.*104C>T		downstream_gene	N/A
	LINC02520	ENST00000829675.1		n.*104C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34483 AN: 152134 Hom.: 4391 Cov.: 34

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.227 AC: 34500 AN: 152252 Hom.: 4403 Cov.: 34 AF XY: 0.227 AC XY: 16900 AN XY: 74450

African (AFR) AF: 0.209 AC: 8694 AN: 41540

American (AMR) AF: 0.203 AC: 3110 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3259 AN: 5182

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4826

European-Finnish (FIN) AF: 0.209 AC: 2216 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14464 AN: 68012

Other (OTH) AF: 0.241 AC: 509 AN: 2114

Alfa AF: 0.219 Hom.: 16384

Bravo AF: 0.226

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.15
DANN	Benign	0.75
PhyloP100		-0.78

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs914351;

hg19: chr6-37518181;