rs9285110

Variant names:

• chr13-20293053-T-C
• rs9285110

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 0.46 in 151,968 control chromosomes in the GnomAD database, including 16,593 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 0.46 (16593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.460 AC: 69897 AN: 151850 Hom.: 16590 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.460 AC: 69935 AN: 151968 Hom.: 16593 Cov.: 32 AF XY: 0.459 AC XY: 34053 AN XY: 74268

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.462

Alfa AF: 0.429 Hom.: 18788

Bravo AF: 0.479

Asia WGS AF: 0.441 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285110; hg19: chr13-20867192;