rs9845475

Variant names:

• chr3-32800609-T-G
• rs9845475

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 0.11 in 152,006 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

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 (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.110 AC: 16684 AN: 151888 Hom.: 1052 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.110 AC: 16703 AN: 152006 Hom.: 1052 Cov.: 31 AF XY: 0.110 AC XY: 8157 AN XY: 74304

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0889

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.109

Alfa AF: 0.135 Hom.: 1892

Bravo AF: 0.107

Asia WGS AF: 0.0620 AC: 217 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	3.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9845475; hg19: chr3-32842101;