20-34150529-G-A

Position:

• chr20-34150529-G-A

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 0.693 in 152,130 control chromosomes in the GnomAD database, including 38,257 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 (38257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105261 AN: 152012 Hom.: 38199 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.693 AC: 105371 AN: 152130 Hom.: 38257 Cov.: 32 AF XY: 0.694 AC XY: 51620 AN XY: 74368

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.706

Alfa AF: 0.584 Hom.: 36323

Bravo AF: 0.718

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015363; hg19: chr20-32738335;