rs9490306

Variant names:

• chr6-121495733-C-A
• rs9490306

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 0.154 in 152,060 control chromosomes in the GnomAD database, including 1,909 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 0.15 (1909 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.268 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: 0.155 AC: 23490 AN: 151942 Hom.: 1910 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.154 AC: 23490 AN: 152060 Hom.: 1909 Cov.: 33 AF XY: 0.155 AC XY: 11506 AN XY: 74334

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.143

Alfa AF: 0.155 Hom.: 1715

Bravo AF: 0.150

Asia WGS AF: 0.179 AC: 621 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.87
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9490306; hg19: chr6-121816879;