chr20-47916417-T-C

Variant names:

• chr20-47916417-T-C
• rs2426039

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 0.676 in 151,946 control chromosomes in the GnomAD database, including 35,843 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 0.68 (35843 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102620 AN: 151828 Hom.: 35792 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.676 AC: 102727 AN: 151946 Hom.: 35843 Cov.: 31 AF XY: 0.672 AC XY: 49878 AN XY: 74252

African (AFR) AF: 0.853 AC: 35377 AN: 41456

American (AMR) AF: 0.589 AC: 8989 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2593 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2944 AN: 5162

South Asian (SAS) AF: 0.650 AC: 3125 AN: 4806

European-Finnish (FIN) AF: 0.546 AC: 5767 AN: 10556

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41832 AN: 67918

Other (OTH) AF: 0.662 AC: 1393 AN: 2104

Alfa AF: 0.640 Hom.: 131566

Bravo AF: 0.688

Asia WGS AF: 0.648 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2426039; hg19: chr20-46545161;