rs9305777

Variant names:

• chr21-16650886-C-T
• rs9305777

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 0.0989 in 152,218 control chromosomes in the GnomAD database, including 1,930 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 0.099 (1930 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.0986 AC: 15001 AN: 152100 Hom.: 1917 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0989 AC: 15049 AN: 152218 Hom.: 1930 Cov.: 33 AF XY: 0.0978 AC XY: 7283 AN XY: 74442

African (AFR) AF: 0.290 AC: 12024 AN: 41498

American (AMR) AF: 0.0469 AC: 718 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.169 AC: 874 AN: 5168

South Asian (SAS) AF: 0.0743 AC: 359 AN: 4830

European-Finnish (FIN) AF: 0.00301 AC: 32 AN: 10624

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0116 AC: 791 AN: 68016

Other (OTH) AF: 0.0691 AC: 146 AN: 2114

Alfa AF: 0.0386 Hom.: 2306

Bravo AF: 0.109

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.49
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9305777; hg19: chr21-18023205;