rs6517720

Variant names:

• chr21-16901773-A-G
• rs6517720

Your query was ambiguous. Multiple possible variants found:

• chr21-16901773-A-G
• chr21-16901773-A-T

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 0.737 in 151,976 control chromosomes in the GnomAD database, including 42,652 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 0.74 (42652 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 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: 0.737 AC: 111992 AN: 151856 Hom.: 42639 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.737 AC: 112039 AN: 151976 Hom.: 42652 Cov.: 33 AF XY: 0.737 AC XY: 54695 AN XY: 74258

African (AFR) AF: 0.528 AC: 21862 AN: 41426

American (AMR) AF: 0.786 AC: 11994 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2779 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3363 AN: 5144

South Asian (SAS) AF: 0.715 AC: 3451 AN: 4826

European-Finnish (FIN) AF: 0.836 AC: 8827 AN: 10560

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.842 AC: 57251 AN: 67986

Other (OTH) AF: 0.753 AC: 1585 AN: 2106

Alfa AF: 0.723 Hom.: 2560

Bravo AF: 0.726

Asia WGS AF: 0.655 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.66
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6517720; hg19: chr21-18274093;