20-39909900-G-T

Position:

• chr20-39909900-G-T

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 0.212 in 152,040 control chromosomes in the GnomAD database, including 3,957 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 0.21 (3957 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39909900G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32236 AN: 151922 Hom.: 3956 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.212 AC: 32247 AN: 152040 Hom.: 3957 Cov.: 32 AF XY: 0.216 AC XY: 16030 AN XY: 74314

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.178

Alfa AF: 0.233 Hom.: 5746

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11699371; hg19: chr20-38538542;