chr20-2097098-G-C

Position:

• chr20-2097098-G-C

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 0.492 in 152,052 control chromosomes in the GnomAD database, including 23,060 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 0.49 (23060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 (EAS) allele frequency at 95% confidence interval = 0.903 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: 0.492 AC: 74730 AN: 151934 Hom.: 23016 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.492 AC: 74826 AN: 152052 Hom.: 23060 Cov.: 32 AF XY: 0.500 AC XY: 37142 AN XY: 74328

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.467

Alfa AF: 0.380 Hom.: 1999

Bravo AF: 0.525

Asia WGS AF: 0.778 AC: 2704 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	0.43
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1418032; hg19: chr20-2077744;