20-2097098-G-C

Variant names:

• chr20-2097098-G-C
• rs1418032

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;