20-58088218-T-C

Position:

• chr20-58088218-T-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 0.298 in 152,180 control chromosomes in the GnomAD database, including 8,512 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 0.30 (8512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.298 AC: 45301 AN: 152062 Hom.: 8518 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.298 AC: 45279 AN: 152180 Hom.: 8512 Cov.: 32 AF XY: 0.289 AC XY: 21526 AN XY: 74418

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.0524

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.321

Alfa AF: 0.416 Hom.: 23802

Bravo AF: 0.288

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.014
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6070346; hg19: chr20-56663274;