rs719721

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC105372666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372666	XR_001754670.2	n.425+18306A>G		intron_variant	Intron 3 of 11
LOC105372666	XR_001754671.2	n.425+18306A>G		intron_variant	Intron 3 of 6
LOC105372666	XR_007067652.1	n.462+18306A>G		intron_variant	Intron 4 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000454600.1	n.335+3599A>G		intron_variant	Intron 4 of 6	3
LINC01524	ENST00000653220.1	n.429+18306A>G		intron_variant	Intron 3 of 3
LINC01524	ENST00000655073.1	n.367+18306A>G		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.290

Alfa AF: 0.275 Hom.: 3205

Bravo AF: 0.296

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719721; hg19: chr20-50975497;