20-12893937-T-C

Variant names:

• chr20-12893937-T-C
• rs2073233
• ENST00000456265.1:n.1669+410A>G

Variant summary

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

The ENST00000456265.1(LINC01722):​n.1669+410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,974 control chromosomes in the GnomAD database, including 15,040 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 0.44 (15040 hom., cov: 32)
• Consequence: LINC01722 ENST00000456265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

Genes affected

LINC01722 (HGNC:52510): (long intergenic non-protein coding RNA 1722)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01722	NR_109868.1	n.1669+410A>G		intron_variant	Intron 9 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01722	ENST00000456265.1	n.1669+410A>G		intron_variant	Intron 9 of 11	1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66966 AN: 151856 Hom.: 15032 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.441 AC: 67000 AN: 151974 Hom.: 15040 Cov.: 32 AF XY: 0.443 AC XY: 32937 AN XY: 74286

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.408

Alfa AF: 0.416 Hom.: 30665

Bravo AF: 0.439

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2073233; hg19: chr20-12874585;