chr20-24065596-C-T

Position:

• chr20-24065596-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664459.1(LINC01721):​n.121+1088C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,060 control chromosomes in the GnomAD database, including 6,705 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 0.20 (6705 hom., cov: 32)
• Consequence: LINC01721 ENST00000664459.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01721	ENST00000664459.1	n.121+1088C>T		intron_variant, non_coding_transcript_variant
LINC01721	ENST00000657180.1	n.191-127C>T		intron_variant, non_coding_transcript_variant
LINC01721	ENST00000669143.1	n.190+1088C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30090 AN: 151940 Hom.: 6671 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.198 AC: 30175 AN: 152060 Hom.: 6705 Cov.: 32 AF XY: 0.194 AC XY: 14404 AN XY: 74336

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.0838

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.168

Alfa AF: 0.0373 Hom.: 66

Bravo AF: 0.221

Asia WGS AF: 0.202 AC: 701 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	1.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6036630; hg19: chr20-24046233;