20-3685839-G-A

Position:

• chr20-3685839-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 0.393 in 152,042 control chromosomes in the GnomAD database, including 11,738 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 0.39 (11738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 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: 0.393 AC: 59725 AN: 151924 Hom.: 11722 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.393 AC: 59778 AN: 152042 Hom.: 11738 Cov.: 33 AF XY: 0.389 AC XY: 28907 AN XY: 74324

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.372

Alfa AF: 0.393 Hom.: 1476

Bravo AF: 0.392

Asia WGS AF: 0.379 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs535964; hg19: chr20-3666486;