rs9289536

Positions:

• chr3-93829635-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 0.778 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.750

Alfa AF: 0.792 Hom.: 44543

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9289536; hg19: chr3-93548479;