20-55933455-T-G

Position:

• chr20-55933455-T-G

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 0.487 in 151,978 control chromosomes in the GnomAD database, including 18,978 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 (18978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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: 0.487 AC: 73982 AN: 151860 Hom.: 18972 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.487 AC: 74023 AN: 151978 Hom.: 18978 Cov.: 32 AF XY: 0.494 AC XY: 36696 AN XY: 74286

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.470

Alfa AF: 0.491 Hom.: 37334

Bravo AF: 0.485

Asia WGS AF: 0.711 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4811645; hg19: chr20-54508511;