chr20-7869280-A-G

Position:

• chr20-7869280-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 0.335 in 152,126 control chromosomes in the GnomAD database, including 13,916 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 0.33 (13916 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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: 0.334 AC: 50772 AN: 152008 Hom.: 13870 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.335 AC: 50890 AN: 152126 Hom.: 13916 Cov.: 33 AF XY: 0.333 AC XY: 24785 AN XY: 74370

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.0818

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.322

Alfa AF: 0.167 Hom.: 6198

Bravo AF: 0.369

Asia WGS AF: 0.503 AC: 1747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
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: rs2205824; hg19: chr20-7849927;