20-17808576-T-C

Variant names:

• chr20-17808576-T-C
• rs2143544

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;