20-2097098-G-C

Variant names:

• chr20-2097098-G-C
• rs1418032

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.814 AC: 33770 AN: 41492

American (AMR) AF: 0.564 AC: 8626 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 890 AN: 3470

East Asian (EAS) AF: 0.925 AC: 4796 AN: 5184

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4816

European-Finnish (FIN) AF: 0.319 AC: 3367 AN: 10542

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19240 AN: 67946

Other (OTH) AF: 0.467 AC: 987 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1418032; hg19: chr20-2077744;