20-17808576-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 0.7 in 151,970 control chromosomes in the GnomAD database, including 38,781 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 0.70 (38781 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106218 AN: 151852 Hom.: 38715 Cov.: 31

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.700 AC: 106338 AN: 151970 Hom.: 38781 Cov.: 31 AF XY: 0.701 AC XY: 52074 AN XY: 74282

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.680

Alfa AF: 0.642 Hom.: 3870

Bravo AF: 0.716

Asia WGS AF: 0.697 AC: 2426 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	4.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143544; hg19: chr20-17789221;