rs563512

chr9-33216486-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.243 in 152,176 control chromosomes in the GnomAD database, including 7,494 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 0.24 (7494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36917 AN: 152058 Hom.: 7473 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.243 AC: 36980 AN: 152176 Hom.: 7494 Cov.: 32 AF XY: 0.238 AC XY: 17746 AN XY: 74428

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.217

Alfa AF: 0.198 Hom.: 634

Bravo AF: 0.255

Asia WGS AF: 0.215 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.6
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs563512; hg19: chr9-33216484;