chr20-12982070-A-G

Position:

• chr20-12982070-A-G

Variant summary

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

The variant allele was found at a frequency of 0.69 in 151,946 control chromosomes in the GnomAD database, including 36,767 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 (36767 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12982070A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01723	ENST00000669657.1	n.874+14860A>G		intron_variant
LINC01723	ENST00000670547.1	n.877-12840A>G		intron_variant
LINC01723	ENST00000671262.1	n.870+14860A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104728 AN: 151828 Hom.: 36723 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.666

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: 104832 AN: 151946 Hom.: 36767 Cov.: 31 AF XY: 0.692 AC XY: 51367 AN XY: 74282

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.689

Alfa AF: 0.626 Hom.: 34552

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	-1.0
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs364585; hg19: chr20-12962718;