rs9289536

Variant names:

• chr3-93829635-T-C
• rs9289536

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 0.778 in 151,976 control chromosomes in the GnomAD database, including 46,175 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 0.78 (46175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 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: 0.778 AC: 118100 AN: 151858 Hom.: 46131 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.778 AC: 118208 AN: 151976 Hom.: 46175 Cov.: 32 AF XY: 0.780 AC XY: 57939 AN XY: 74272

African (AFR) AF: 0.712 AC: 29528 AN: 41468

American (AMR) AF: 0.798 AC: 12165 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3468

East Asian (EAS) AF: 0.774 AC: 3992 AN: 5158

South Asian (SAS) AF: 0.778 AC: 3752 AN: 4820

European-Finnish (FIN) AF: 0.877 AC: 9293 AN: 10594

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54977 AN: 67922

Other (OTH) AF: 0.750 AC: 1578 AN: 2104

Alfa AF: 0.787 Hom.: 72016

Bravo AF: 0.767

Asia WGS AF: 0.766 AC: 2659 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.036
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9289536; hg19: chr3-93548479;