20-43666079-T-C

Variant names:

• chr20-43666079-T-C
• rs826944

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 0.831 in 147,938 control chromosomes in the GnomAD database, including 51,461 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 0.83 (51461 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 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: 0.831 AC: 122795 AN: 147826 Hom.: 51427 Cov.: 22

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.789

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.831 AC: 122880 AN: 147938 Hom.: 51461 Cov.: 22 AF XY: 0.833 AC XY: 59766 AN XY: 71780

African (AFR) AF: 0.741 AC: 29398 AN: 39680

American (AMR) AF: 0.797 AC: 11774 AN: 14764

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2940 AN: 3464

East Asian (EAS) AF: 0.800 AC: 4020 AN: 5028

South Asian (SAS) AF: 0.828 AC: 3880 AN: 4688

European-Finnish (FIN) AF: 0.927 AC: 8884 AN: 9584

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.879 AC: 59303 AN: 67500

Other (OTH) AF: 0.815 AC: 1657 AN: 2034

Alfa AF: 0.850 Hom.: 2812

Bravo AF: 0.814

Asia WGS AF: 0.793 AC: 2754 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs826944; hg19: chr20-42294719;