chr20-17808576-T-C

Variant names:

• chr20-17808576-T-C
• rs2143544

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 0.7 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
• 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 (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.920 AC: 38205 AN: 41508

American (AMR) AF: 0.662 AC: 10094 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3470

East Asian (EAS) AF: 0.775 AC: 4006 AN: 5166

South Asian (SAS) AF: 0.649 AC: 3125 AN: 4812

European-Finnish (FIN) AF: 0.630 AC: 6634 AN: 10530

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40051 AN: 67932

Other (OTH) AF: 0.680 AC: 1434 AN: 2108

Alfa AF: 0.645 Hom.: 46939

Bravo AF: 0.716

Asia WGS AF: 0.697 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs2143544; hg19: chr20-17789221;