rs34852119

Variant names:

• chr20-795629-A-G
• rs34852119

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 0.0583 in 152,218 control chromosomes in the GnomAD database, including 643 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 0.058 (643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8876 AN: 152100 Hom.: 646 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0583 AC: 8867 AN: 152218 Hom.: 643 Cov.: 32 AF XY: 0.0595 AC XY: 4432 AN XY: 74432

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.0255

Gnomad4 FIN AF: 0.0775

Gnomad4 NFE AF: 0.0644

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0538 Hom.: 43

Bravo AF: 0.0559

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34852119; hg19: chr20-776272;