20-12985441-T-G

Variant names:

• chr20-12985441-T-G
• rs168622
• ENST00000669657.1:n.874+18231T>G

Variant summary

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

The ENST00000669657.1(LINC01723):​n.874+18231T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,128 control chromosomes in the GnomAD database, including 36,863 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 0.69 (36863 hom., cov: 32)
• Consequence: LINC01723 ENST00000669657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 26 publications found

Genes affected

LINC01723 (HGNC:52511): (long intergenic non-protein coding RNA 1723)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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
LINC01723	ENST00000669657.1	n.874+18231T>G		intron_variant	Intron 4 of 4
LINC01723	ENST00000670547.1	n.877-9469T>G		intron_variant	Intron 4 of 5
LINC01723	ENST00000671262.1	n.870+18231T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104931 AN: 152010 Hom.: 36819 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.690 AC: 105035 AN: 152128 Hom.: 36863 Cov.: 32 AF XY: 0.692 AC XY: 51474 AN XY: 74360

African (AFR) AF: 0.833 AC: 34570 AN: 41510

American (AMR) AF: 0.694 AC: 10600 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2974 AN: 5172

South Asian (SAS) AF: 0.681 AC: 3287 AN: 4830

European-Finnish (FIN) AF: 0.667 AC: 7050 AN: 10566

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41927 AN: 67984

Other (OTH) AF: 0.688 AC: 1454 AN: 2112

Alfa AF: 0.660 Hom.: 5694

Bravo AF: 0.695

Asia WGS AF: 0.659 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs168622; hg19: chr20-12966089;