rs9569528

Variant names:

• chr13-56761975-T-C
• rs9569528

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 0.101 in 151,960 control chromosomes in the GnomAD database, including 1,019 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 0.10 (1019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 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: 0.101 AC: 15365 AN: 151842 Hom.: 1022 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0361

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.101 AC: 15369 AN: 151960 Hom.: 1019 Cov.: 32 AF XY: 0.101 AC XY: 7489 AN XY: 74314

African (AFR) AF: 0.170 AC: 7048 AN: 41440

American (AMR) AF: 0.0883 AC: 1348 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0361 AC: 125 AN: 3466

East Asian (EAS) AF: 0.190 AC: 982 AN: 5170

South Asian (SAS) AF: 0.0863 AC: 415 AN: 4808

European-Finnish (FIN) AF: 0.0690 AC: 730 AN: 10584

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0645 AC: 4379 AN: 67916

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.0894 Hom.: 155

Bravo AF: 0.106

Asia WGS AF: 0.142 AC: 492 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.81
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs9569528; hg19: chr13-57336109;