20-33130847-C-T

Variant names:

• chr20-33130847-C-T
• rs6059101

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 0.222 in 152,076 control chromosomes in the GnomAD database, including 4,068 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 0.22 (4068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.222 AC: 33761 AN: 151958 Hom.: 4058 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.222 AC: 33796 AN: 152076 Hom.: 4068 Cov.: 32 AF XY: 0.222 AC XY: 16470 AN XY: 74330

African (AFR) AF: 0.215 AC: 8905 AN: 41490

American (AMR) AF: 0.169 AC: 2583 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3468

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5178

South Asian (SAS) AF: 0.163 AC: 784 AN: 4814

European-Finnish (FIN) AF: 0.312 AC: 3292 AN: 10558

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16188 AN: 67984

Other (OTH) AF: 0.219 AC: 463 AN: 2114

Alfa AF: 0.221 Hom.: 7495

Bravo AF: 0.209

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.86
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs6059101; hg19: chr20-31718653;