20-21811216-T-G

Variant names:

• chr20-21811216-T-G
• rs6047641

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 0.775 in 151,894 control chromosomes in the GnomAD database, including 47,693 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 0.77 (47693 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.905 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: 0.775 AC: 117634 AN: 151776 Hom.: 47687 Cov.: 30

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.775 AC: 117660 AN: 151894 Hom.: 47693 Cov.: 30 AF XY: 0.774 AC XY: 57465 AN XY: 74226

African (AFR) AF: 0.542 AC: 22412 AN: 41366

American (AMR) AF: 0.703 AC: 10734 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3095 AN: 3468

East Asian (EAS) AF: 0.656 AC: 3371 AN: 5140

South Asian (SAS) AF: 0.822 AC: 3942 AN: 4798

European-Finnish (FIN) AF: 0.897 AC: 9486 AN: 10570

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61911 AN: 67974

Other (OTH) AF: 0.796 AC: 1679 AN: 2110

Alfa AF: 0.840 Hom.: 41321

Bravo AF: 0.746

Asia WGS AF: 0.679 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs6047641; hg19: chr20-21791854;