rs9490306

Variant names:

• chr6-121495733-C-A
• rs9490306

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 0.154 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.159 AC: 6590 AN: 41454

American (AMR) AF: 0.113 AC: 1728 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.134 AC: 693 AN: 5174

South Asian (SAS) AF: 0.281 AC: 1353 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1215 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10602 AN: 67974

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.155 Hom.: 2064

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
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs9490306; hg19: chr6-121816879;