20-5466971-A-G

Variant names:

• chr20-5466971-A-G
• rs6053417
• ENST00000593667.2:n.97-2042T>C

Variant summary

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

The ENST00000593667.2(LINC00658):​n.97-2042T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,126 control chromosomes in the GnomAD database, including 26,309 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 0.56 (26309 hom., cov: 32)
• Consequence: LINC00658 ENST00000593667.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 1 publications found

Genes affected

LINC00658 (HGNC:44315): (long intergenic non-protein coding RNA 658)

ENSG00000230563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593667.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00658	ENST00000593667.2	TSL:6	n.97-2042T>C		intron	N/A
	LINC00658	ENST00000600157.6	TSL:5	n.71-2042T>C		intron	N/A
	ENSG00000230563	ENST00000651499.1		n.646+205A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85431 AN: 152008 Hom.: 26269 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.562 AC: 85521 AN: 152126 Hom.: 26309 Cov.: 32 AF XY: 0.563 AC XY: 41847 AN XY: 74362

African (AFR) AF: 0.838 AC: 34788 AN: 41516

American (AMR) AF: 0.501 AC: 7658 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1776 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2290 AN: 5172

South Asian (SAS) AF: 0.499 AC: 2406 AN: 4822

European-Finnish (FIN) AF: 0.502 AC: 5305 AN: 10572

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29749 AN: 67972

Other (OTH) AF: 0.519 AC: 1098 AN: 2116

Alfa AF: 0.474 Hom.: 29264

Bravo AF: 0.574

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6053417; hg19: chr20-5447617;