rs563353

Variant names:

• chr9-33216430-G-C
• rs563353

Your query was ambiguous. Multiple possible variants found:

• chr9-33216430-G-C
• chr9-33216430-G-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 0.328 in 152,072 control chromosomes in the GnomAD database, including 10,160 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 0.33 (10160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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: 0.327 AC: 49738 AN: 151954 Hom.: 10132 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.328 AC: 49817 AN: 152072 Hom.: 10160 Cov.: 32 AF XY: 0.323 AC XY: 23989 AN XY: 74350

African (AFR) AF: 0.586 AC: 24280 AN: 41454

American (AMR) AF: 0.241 AC: 3683 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1399 AN: 5168

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10584

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15000 AN: 67980

Other (OTH) AF: 0.323 AC: 681 AN: 2110

Alfa AF: 0.287 Hom.: 931

Bravo AF: 0.340

Asia WGS AF: 0.345 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs563353; hg19: chr9-33216428; COSMIC: COSV65689107;