ENST00000510065.1:n.167-56429T>C

Variant names:

• chr5-12970600-A-G
• rs1561364
• ENST00000510065.1:n.167-56429T>C

Variant summary

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

The ENST00000510065.1(LINC02220):​n.167-56429T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,208 control chromosomes in the GnomAD database, including 61,456 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 0.88 (61456 hom., cov: 33)
• Consequence: LINC02220 ENST00000510065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 0 publications found

Genes affected

LINC02220 (HGNC:53087): (long intergenic non-protein coding RNA 2220)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510065.1. 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
	LINC02220	NR_147005.1		n.167-56429T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02220	ENST00000510065.1	TSL:5	n.167-56429T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133957 AN: 152090 Hom.: 61428 Cov.: 33

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.881 AC: 134034 AN: 152208 Hom.: 61456 Cov.: 33 AF XY: 0.886 AC XY: 65946 AN XY: 74418

African (AFR) AF: 0.591 AC: 24508 AN: 41466

American (AMR) AF: 0.952 AC: 14547 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3340 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5180

South Asian (SAS) AF: 0.999 AC: 4824 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67880 AN: 68038

Other (OTH) AF: 0.914 AC: 1929 AN: 2110

Alfa AF: 0.944 Hom.: 18261

Bravo AF: 0.864

Asia WGS AF: 0.976 AC: 3384 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.3
DANN	Benign	0.75
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1561364; hg19: chr5-12970712;