20-24077771-C-T

Variant names:

• chr20-24077771-C-T
• rs6049375
• ENST00000664459.1:n.121+13263C>T

Variant summary

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

The ENST00000664459.1(LINC01721):​n.121+13263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,048 control chromosomes in the GnomAD database, including 4,680 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 0.18 (4680 hom., cov: 32)
• Consequence: LINC01721 ENST00000664459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 12 publications found

Genes affected

LINC01721 (HGNC:52508): (long intergenic non-protein coding RNA 1721)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01721	ENST00000664459.1	n.121+13263C>T		intron_variant	Intron 2 of 5
LINC01721	ENST00000669143.1	n.190+13263C>T		intron_variant	Intron 2 of 4
LINC01721	ENST00000753590.1	n.183+13263C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26719 AN: 151930 Hom.: 4666 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.0933

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.176 AC: 26776 AN: 152048 Hom.: 4680 Cov.: 32 AF XY: 0.173 AC XY: 12825 AN XY: 74346

African (AFR) AF: 0.451 AC: 18682 AN: 41432

American (AMR) AF: 0.0935 AC: 1428 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0933 AC: 324 AN: 3472

East Asian (EAS) AF: 0.174 AC: 894 AN: 5152

South Asian (SAS) AF: 0.124 AC: 597 AN: 4810

European-Finnish (FIN) AF: 0.0358 AC: 379 AN: 10588

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0592 AC: 4025 AN: 68008

Other (OTH) AF: 0.151 AC: 319 AN: 2106

Alfa AF: 0.103 Hom.: 5500

Bravo AF: 0.194

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6049375; hg19: chr20-24058407; COSMIC: COSV53316824;