20-2803626-T-G

Variant names:

• chr20-2803626-T-G
• rs107130

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 0.883 in 152,060 control chromosomes in the GnomAD database, including 59,416 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 0.88 (59416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.883 AC: 134223 AN: 151942 Hom.: 59365 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.883 AC: 134333 AN: 152060 Hom.: 59416 Cov.: 31 AF XY: 0.885 AC XY: 65748 AN XY: 74308

African (AFR) AF: 0.873 AC: 36163 AN: 41446

American (AMR) AF: 0.901 AC: 13771 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2955 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5160 AN: 5172

South Asian (SAS) AF: 0.908 AC: 4370 AN: 4814

European-Finnish (FIN) AF: 0.876 AC: 9247 AN: 10560

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.879 AC: 59807 AN: 68008

Other (OTH) AF: 0.891 AC: 1879 AN: 2108

Alfa AF: 0.883 Hom.: 7369

Bravo AF: 0.886

Asia WGS AF: 0.951 AC: 3307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs107130; hg19: chr20-2784272;