20-6999988-G-T

Position:

• chr20-6999988-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 0.0405 in 152,090 control chromosomes in the GnomAD database, including 140 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 0.040 (140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0581 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0405 AC: 6154 AN: 151972 Hom.: 140 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0405 AC: 6154 AN: 152090 Hom.: 140 Cov.: 32 AF XY: 0.0395 AC XY: 2933 AN XY: 74342

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0523 Hom.: 118

Bravo AF: 0.0382

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085820; hg19: chr20-6980635;