rs719721

Variant names:

• chr20-52358958-A-G
• rs719721
• ENST00000454600.1:n.335+3599A>G

Variant summary

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

The ENST00000454600.1(LINC01524):​n.335+3599A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,130 control chromosomes in the GnomAD database, including 6,329 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 0.29 (6329 hom., cov: 32)
• Consequence: LINC01524 ENST00000454600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 0 publications found

Genes affected

LINC01524 (HGNC:51228): (long intergenic non-protein coding RNA 1524)

LOC105372666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454600.1. 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
	LINC01524	ENST00000454600.1	TSL:3	n.335+3599A>G		intron	N/A
	LINC01524	ENST00000653220.2		n.460+18306A>G		intron	N/A
	LINC01524	ENST00000655073.2		n.367+18306A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43378 AN: 152012 Hom.: 6312 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.286 AC: 43441 AN: 152130 Hom.: 6329 Cov.: 32 AF XY: 0.281 AC XY: 20895 AN XY: 74374

African (AFR) AF: 0.325 AC: 13469 AN: 41484

American (AMR) AF: 0.304 AC: 4650 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5168

South Asian (SAS) AF: 0.195 AC: 939 AN: 4826

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10584

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18710 AN: 68004

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.276 Hom.: 3584

Bravo AF: 0.296

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.85
PhyloP100		0.015

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: rs719721;

hg19: chr20-50975497;