rs9560105

Variant names:

• chr13-111523016-T-A
• rs9560105

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 0.249 in 152,152 control chromosomes in the GnomAD database, including 4,942 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 0.25 (4942 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.250 AC: 37953 AN: 152034 Hom.: 4946 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.249 AC: 37952 AN: 152152 Hom.: 4942 Cov.: 33 AF XY: 0.251 AC XY: 18659 AN XY: 74376

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.289

Alfa AF: 0.264 Hom.: 684

Bravo AF: 0.247

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9560105; hg19: chr13-112175363;