chr20-24231409-T-C

Variant names:

• chr20-24231409-T-C
• rs1120902
• ENST00000753590.1:n.428+11707T>C

Variant summary

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

The ENST00000753590.1(LINC01721):​n.428+11707T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,016 control chromosomes in the GnomAD database, including 26,490 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 0.59 (26490 hom., cov: 33)
• Consequence: LINC01721 ENST00000753590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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	ENST00000753590.1	n.428+11707T>C		intron_variant	Intron 4 of 4
LINC01721	ENST00000753591.1	n.935+11707T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89387 AN: 151898 Hom.: 26473 Cov.: 33

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.588 AC: 89446 AN: 152016 Hom.: 26490 Cov.: 33 AF XY: 0.592 AC XY: 43972 AN XY: 74308

African (AFR) AF: 0.660 AC: 27359 AN: 41476

American (AMR) AF: 0.528 AC: 8073 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1806 AN: 3466

East Asian (EAS) AF: 0.695 AC: 3586 AN: 5162

South Asian (SAS) AF: 0.547 AC: 2642 AN: 4826

European-Finnish (FIN) AF: 0.639 AC: 6746 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37458 AN: 67930

Other (OTH) AF: 0.573 AC: 1212 AN: 2114

Alfa AF: 0.575 Hom.: 3290

Bravo AF: 0.581

Asia WGS AF: 0.609 AC: 2116 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.31
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1120902; hg19: chr20-24212045;