rs9569528

Positions:

• chr13-56761975-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 0.101 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0883

Gnomad4 ASJ AF: 0.0361

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0863

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0873 Hom.: 143

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9569528; hg19: chr13-57336109;